99 and 01 Mustang Cobra FAQ Basic Info
Q. What is different between the 99/01 and 96-98 4.6 4 valve engines?
A. The 96-98 mustang cobra comes with a 281 cube 4 valve engine. It sports an aluminum block with a 3.55 bore/3.54 stroke. This block has 6 bolt main caps and is cast by Teksid in Italy. This block also has jack screws (to positively locate the main caps from the side) and smaller side bolts that go through the jack screws. The forged crankshaft is a kellog piece and has an 8 bolt flywheel bolt pattern. The powdered metal rods and hypereutectic pistons are the weak points. The pistons have a 3cc dish. The 96-98 is also equipped with the B heads. They are also known as swirl port heads. These heads have 2 intake ports per cylinder, with an Intake runner control (IMRC) to block off the secondary intake ports until the engine reaches 3250 rpm to promote torque production. The camshafts produce a touch more lowend power then peak power to make the engine more responsive down low. The long runner intake is a 2 piece unit with a sidemount dual 57mm throttle body.
The 99/01 motor has a very similar bottom end. The only differences include larger side bolts with no jack screws, a different sized knock sensor bolt, and the possibility of a different block. The new block is the Windsor Aluminum Plant block (wap block for short). This block has visible ribbing that looks stronger, but the case itself is thinner, making it 5lbs lighter, but weaker overall. The teksid block is the one to have, but the wap will still stand over 700bhp (I have been over this level for more than a year with a wap block). The heads are single port, tumble port “C” Heads. They have a smaller intake port and larger more oval exhaust port in order to make the engine more responsive. The cams are ground more for top end power. The 2 piece intake also has a side mount 57mm throttle body and long runners for torque production. The timing gear is pretty similar with slight differences. The valve covers and timing covers are different. The ignition on the 99/01 motor is a coil on plug system vs 2 coil packs and plug wires on the 96-98. The COP system delivers a stronger spark with less maintenance.
Q. What spark plugs should I use on my 99/01 motor?
A. That depends greatly on the setup. For a basically stock motor, the factory spec’ed plug is a platinum 32 series motorcraft plug. While decent for long life, its not necessarily a performance plug. A switch to copper will give better performance, a cheaper price, at the cost of having to change plugs more often (about every 30k miles). Copper replacements for the stock heat range are Autolite 764s, and ngk tr55s. Do not use the bosch platinum series (either 2 or 4). The recommended gap for naturally aspirated applications is .052 to .056
For wilder setups making over 300rwhp, it might be necessary to go to a colder plug (also for those in very warm climates). The 1 step colder plugs would be the NGK tr6 or I believe the autolite 103 plugs. Ford makes a lovely 1 heat range colder copper plug called the awsfa-22c. this is often regarded as the holy grail plug.
For blown cars with under 10psi, the 1 heat range colder plugs will work well. Start the gap at .035 and make it smaller if you are blowing out the spark (misfires under boost, lots of grey smoke, loss in pull)
For blown cars with higher boost levels, 2 heat range plugs may be needed. These are NGK tr7s or awsfa-12c plugs. I personally run the 12c plugs at a .028 gap with a completely stock ignition. They have been working well.
Q. What exhaust should I run on my 99/01?
A. Tricky question due to personal preference on powerband and sound. There are 3 exhaust categories. 1. Headers, 2. mid pipe, 3 catback. For headers, you can either get shorties, mid lengths or longtubes. Shorties will make the least torque, but are smog legal. They are all a bitch to install, so it won’t make much difference. The only shortie headers to get are JBA. The 1 5/8th size is best for most cobras. FRPP shortie headers are absolute garbage and a waste of money. As far as I know, only bassani makes midlengths and there isn’t that much info on them. If I were going to go to midlengths id go all the way to long tubes. Long tubes have low ground clearance and many brands (aside from hooker and kooks I believe) will require loosening to remove the transmission. Long tube headers will provide a nice boost in low end torque and slightly better gains then other headers up top. DO NOT BUY MAC HEADERS, AND IF YOU DO, CLEAN THE INSIDES OUT VERY WELL BEFORE.
Mid pipe is a toss up. Some like x pipes, others h pipes and others the prochamber. The bottom line is that they all have very similar power gains (about 10rwhp or so) so buy what you think sounds the best.
As far as catback, its pretty much like the midpipe. They all give fairly modest power gains so go with what you think sounds the best. Keep in mind that these will need to be specific to the 99/01 because of the rear suspension so something from and older model won’t fit.
Q. Oil and Oil filter?
A. This question is dependant on both climate, wallet size, and driving style. The spec’ed oil for 99 cobras is 5w-30. For 01s its 5w-20. It will not make a difference which ones you use. Since all these cars are out of the factory warranty, use whatever one is easier to find. If you live in a very hot climate and like to beat on the car, go for something a little thicker. If you live in a cold area, get a thinner oil in order to get the valvetrain lubricated quicker. Do not run anything thicker than a 10w-40. This is not your buddies small block chevy with bearing clearance so thick you could shove a pen through it. You can’t run such thick oil on a mod motor. If you want to get the absolute best oil, go for either german castrol (says made in germany on the back) or amsoil. If you have a midrange budget, get mobil 1 or royal purple. If you want synthetic but don’t have a ton of cash, valvoline or castrol syntec is ok. If you don’t care, put some normal dino oil in.
Oil filters. There are many on the market. All of them are ok except for FRAM. FRAM is junk and the only place it should be is on your lawn mower. The most popular are the Motorcraft Fl820s filter, the K&N one and the Mobil M1 filter.
Oil change frequency and oil level are too controversial so I’ll only tell you what I do. I change my mobil 1 synthetic at 3k miles and run 7 quarts.
Q. When to change my fuel filter, where is it, and how?
A. The fuel filter should be replaced on a normal cobra every 30k or so. For a blown car move that down to every 10k. It’s a 17 dollar part, so replace it often. It is located on the passenger side, above the irs, about 6 inches from the tank. Little silver canister. You need a ford fuel line disconnect tool. It’s a metal piece that looks like a scissor. The basics of the change are this. Put car on ramps or jackstands in rear. Use screwdriver to pop off safety clips. Use tool to disconnect line going to engine. Loosen hose clamp. Remove line from other side. Pop filter out. Replace filter, connect lines, and reinstall safety clips.
Q. What size are our injectors?
A. All modular cobras until 03 run high impedence 24lb injectors. The 03 runs 39lb injectors. All aftermarket injectors have the 96-98 electronic plug. PHP and CPR as well as a bunch of vendors sell adapters to run larger injectors on our setups. 60s are the largest, most readily available high impedence injectors. They also offer good driveability. The Stock computer can not run low impedence injectors without a driver. This is expensive and kind of useless since 60s will support about 700rwhp. Standalone fuel systems like FAST or DFI can run both low and high impedence.
Q. What temp is the stock thermostat
A. Right around 195 degrees
Q. What are good easy bolt ons?
A. Underdrive pullies, a cold air intake, exhaust, gears, a timing adjuster or tune, and a ported intake work well.
Q. What are useless bolt ons?
A. Throttle body and maf are ones that 90% of cars don’t need.
Q. I want to do cams on my basically stock cobra, good idea?
A. No, it’s a bad idea. Cams are expensive (900), they usually require springs (600) and are a pain to install (800), so they are not a good idea. They don’t add much power on a basically stock cobra and are really a mod to do after you’ve done bolt ons.
Q. Tranny fluid, whats the best?
A. Hard to say. Most people use either GM synchromesh (Pennzoil synchromesh is the same thing but cheaper), some use redline and others use royal purple. The stock fluid is ATF (not mercon V though)
Q. How Do I change my tranny fluid?
A. Jack up the car until it is level front and back. Get a drain pan and find the fill and drain holes. On the t45 they are on the tailshaft housing and the fill and drain are both on the passenger side of the tranny. On the tr3650 the drain is on the bottom, the fill is on the passenger side. MAKE SURE TO LOOSEN THE FILL PLUG FIRST SO YOU KNOW YOU CAN REMOVE IT. So remove the fill plug, then remove the drain plug using a 3/8s ratchet. let it drain for 20 minutes or so and then reinstall the drain plug.
Now using about 3.2 quarts of tranny fluid, get a 3/8th outerdiameter hose and a funnel. Remove the shift knob, the shift boot (pull up from the plastic surround, should come out easy.) don't remove the electrical connections, just let it hang off the side. now, remove the 4 8mm bolts that hold the rubber boot down. pull that off the shifer and then snake the hose down into the fill hole. pour the fluid in, and then reinstall the fill plug. seems complicated but its not.
Q. My engine squeaks when cold?
A. Most likely a belt tensioner pulley bearing. Also possibly an idler pulley bearing (1 on a 99, 2 on an 01). Go to a local bearing shop and have them pop a new NTN 6502 bearing in. should cost about 5 bux and you’re set.
Q. My engine won’t idle/dies when I come to a stop/or revs up when I push the clutch in.
A. 90% of the time this is caused by a dirty or faulty Idle air Control (IAC)motor. This is the silver canister located on the passenger side of the intake right by the throttle body. It is held on by 2 8mm bolts and an electrical connector. To clean, take it off, spray it with brake cleaner and either swish it around or use a q tip to clean it. If that doesn’t work, try replacing it. About $80 at ford, around 60 at parts store. Quality of parts store parts unknown.
Q. My engine runs crappy, low power, and backfiring?
A. Try cleaning the maf. It’s the electrical sensor located right after your air box. It requires a tamper-proof torx bit to remove and electrical cleaner to clean. You can figure out the rest.
Q. What should my fuel pressure be at idle, cruise, and WOT?
A. Fuel pressure is always delta pressure- (manifold pressure/2). So at idle, you should see about 20 inches of vaccum. Delta pressure is 39 psi, so you should see about 30 or so psi at idle. This works for all varying levels of throttle. At WOT or zero vaccum, you should see 39psi of fuel pressure.
Q. What should my oil pressure be?
A. the stock oil pressure gauge is useless. Its an on/off switch that reads 60% pressure over 6 psi and zero below. On an aftermarket gauge, you should see about 90psi at cold start. 25 psi at hot idle, and above 75 at 3000rpm cruise. Ford specs are 20 to 45 psi at 1500rpm.
Q. When on the highway at around 2000rpm and I let off the gas, and then get back on it quickly, i get a clunk, what is that?
A. That is most likely the backlash in the gears. They tend to be a little sloppy in stock form so they can clunk on transition from coast to drive.
Q. What gears should I get for my car?
A. that depends on a few things.
1. How is the car used
2. How is the car set up(NA, spray, boost)
3. traction
4. personal preference.
If you use the car daily, and drive a lot of highway, something like a 4.30 gear might be a bit steep. However, for a drag race car that is barely ever street driven, 3.73s are not enough. these cars are not like a 5.0, they make weak torque down low and most power up high, so you need more gear (especially since they are heavy). So, as a general rule of thumb, if you do just about all highway driving and don't race it, 3.73s or 4.10s are good. If you do street strip stuff, then 4.10s or 4.30s are good. If you do primarily drag racing, 4.30s or 4.56s are the way to go. Keep in mind that with 4.56s you may need to grind the cross pin to get it to fit.
2. The more power you have, the less gear you are likely to need. NA cars need the most gear, centrifugal blown cars need the second most, turbo and nitrous cars need less, and roots blown cars really don't need much because of the massive down low torque. However, its back to personal preference.
3. If your car can't hook, all the gear in the world won't help. So if you want gears and have decent power, don't expect it to hook without suspension work. If you don't want to touch the suspension, adding a ton of gear might not help at the track (at least get some better tires)
4. Personal preference is just that; personal. Some people don't like seeing 2700rpm at a 70mph cruise and for others thats nothing. some don't like shifting after 30 feet out of first gear. Some people don't like worse gas mileage around town that come from gears.
For reference with stock tire diameter and tranny, 70mph with stock gears is about 2100rpm. 70mph with 3.73s is like 2400, 4.10s is like 2650, with 4.30s its like 2790 and with 4.56s its closer to 3k.
1999 Belt Routing
2001 Belt Routing
Blown 99 belt routing
Q. What is different between the 99/01 and 96-98 4.6 4 valve engines?
A. The 96-98 mustang cobra comes with a 281 cube 4 valve engine. It sports an aluminum block with a 3.55 bore/3.54 stroke. This block has 6 bolt main caps and is cast by Teksid in Italy. This block also has jack screws (to positively locate the main caps from the side) and smaller side bolts that go through the jack screws. The forged crankshaft is a kellog piece and has an 8 bolt flywheel bolt pattern. The powdered metal rods and hypereutectic pistons are the weak points. The pistons have a 3cc dish. The 96-98 is also equipped with the B heads. They are also known as swirl port heads. These heads have 2 intake ports per cylinder, with an Intake runner control (IMRC) to block off the secondary intake ports until the engine reaches 3250 rpm to promote torque production. The camshafts produce a touch more lowend power then peak power to make the engine more responsive down low. The long runner intake is a 2 piece unit with a sidemount dual 57mm throttle body.
The 99/01 motor has a very similar bottom end. The only differences include larger side bolts with no jack screws, a different sized knock sensor bolt, and the possibility of a different block. The new block is the Windsor Aluminum Plant block (wap block for short). This block has visible ribbing that looks stronger, but the case itself is thinner, making it 5lbs lighter, but weaker overall. The teksid block is the one to have, but the wap will still stand over 700bhp (I have been over this level for more than a year with a wap block). The heads are single port, tumble port “C” Heads. They have a smaller intake port and larger more oval exhaust port in order to make the engine more responsive. The cams are ground more for top end power. The 2 piece intake also has a side mount 57mm throttle body and long runners for torque production. The timing gear is pretty similar with slight differences. The valve covers and timing covers are different. The ignition on the 99/01 motor is a coil on plug system vs 2 coil packs and plug wires on the 96-98. The COP system delivers a stronger spark with less maintenance.
Q. What spark plugs should I use on my 99/01 motor?
A. That depends greatly on the setup. For a basically stock motor, the factory spec’ed plug is a platinum 32 series motorcraft plug. While decent for long life, its not necessarily a performance plug. A switch to copper will give better performance, a cheaper price, at the cost of having to change plugs more often (about every 30k miles). Copper replacements for the stock heat range are Autolite 764s, and ngk tr55s. Do not use the bosch platinum series (either 2 or 4). The recommended gap for naturally aspirated applications is .052 to .056
For wilder setups making over 300rwhp, it might be necessary to go to a colder plug (also for those in very warm climates). The 1 step colder plugs would be the NGK tr6 or I believe the autolite 103 plugs. Ford makes a lovely 1 heat range colder copper plug called the awsfa-22c. this is often regarded as the holy grail plug.
For blown cars with under 10psi, the 1 heat range colder plugs will work well. Start the gap at .035 and make it smaller if you are blowing out the spark (misfires under boost, lots of grey smoke, loss in pull)
For blown cars with higher boost levels, 2 heat range plugs may be needed. These are NGK tr7s or awsfa-12c plugs. I personally run the 12c plugs at a .028 gap with a completely stock ignition. They have been working well.
Q. What exhaust should I run on my 99/01?
A. Tricky question due to personal preference on powerband and sound. There are 3 exhaust categories. 1. Headers, 2. mid pipe, 3 catback. For headers, you can either get shorties, mid lengths or longtubes. Shorties will make the least torque, but are smog legal. They are all a bitch to install, so it won’t make much difference. The only shortie headers to get are JBA. The 1 5/8th size is best for most cobras. FRPP shortie headers are absolute garbage and a waste of money. As far as I know, only bassani makes midlengths and there isn’t that much info on them. If I were going to go to midlengths id go all the way to long tubes. Long tubes have low ground clearance and many brands (aside from hooker and kooks I believe) will require loosening to remove the transmission. Long tube headers will provide a nice boost in low end torque and slightly better gains then other headers up top. DO NOT BUY MAC HEADERS, AND IF YOU DO, CLEAN THE INSIDES OUT VERY WELL BEFORE.
Mid pipe is a toss up. Some like x pipes, others h pipes and others the prochamber. The bottom line is that they all have very similar power gains (about 10rwhp or so) so buy what you think sounds the best.
As far as catback, its pretty much like the midpipe. They all give fairly modest power gains so go with what you think sounds the best. Keep in mind that these will need to be specific to the 99/01 because of the rear suspension so something from and older model won’t fit.
Q. Oil and Oil filter?
A. This question is dependant on both climate, wallet size, and driving style. The spec’ed oil for 99 cobras is 5w-30. For 01s its 5w-20. It will not make a difference which ones you use. Since all these cars are out of the factory warranty, use whatever one is easier to find. If you live in a very hot climate and like to beat on the car, go for something a little thicker. If you live in a cold area, get a thinner oil in order to get the valvetrain lubricated quicker. Do not run anything thicker than a 10w-40. This is not your buddies small block chevy with bearing clearance so thick you could shove a pen through it. You can’t run such thick oil on a mod motor. If you want to get the absolute best oil, go for either german castrol (says made in germany on the back) or amsoil. If you have a midrange budget, get mobil 1 or royal purple. If you want synthetic but don’t have a ton of cash, valvoline or castrol syntec is ok. If you don’t care, put some normal dino oil in.
Oil filters. There are many on the market. All of them are ok except for FRAM. FRAM is junk and the only place it should be is on your lawn mower. The most popular are the Motorcraft Fl820s filter, the K&N one and the Mobil M1 filter.
Oil change frequency and oil level are too controversial so I’ll only tell you what I do. I change my mobil 1 synthetic at 3k miles and run 7 quarts.
Q. When to change my fuel filter, where is it, and how?
A. The fuel filter should be replaced on a normal cobra every 30k or so. For a blown car move that down to every 10k. It’s a 17 dollar part, so replace it often. It is located on the passenger side, above the irs, about 6 inches from the tank. Little silver canister. You need a ford fuel line disconnect tool. It’s a metal piece that looks like a scissor. The basics of the change are this. Put car on ramps or jackstands in rear. Use screwdriver to pop off safety clips. Use tool to disconnect line going to engine. Loosen hose clamp. Remove line from other side. Pop filter out. Replace filter, connect lines, and reinstall safety clips.
Q. What size are our injectors?
A. All modular cobras until 03 run high impedence 24lb injectors. The 03 runs 39lb injectors. All aftermarket injectors have the 96-98 electronic plug. PHP and CPR as well as a bunch of vendors sell adapters to run larger injectors on our setups. 60s are the largest, most readily available high impedence injectors. They also offer good driveability. The Stock computer can not run low impedence injectors without a driver. This is expensive and kind of useless since 60s will support about 700rwhp. Standalone fuel systems like FAST or DFI can run both low and high impedence.
Q. What temp is the stock thermostat
A. Right around 195 degrees
Q. What are good easy bolt ons?
A. Underdrive pullies, a cold air intake, exhaust, gears, a timing adjuster or tune, and a ported intake work well.
Q. What are useless bolt ons?
A. Throttle body and maf are ones that 90% of cars don’t need.
Q. I want to do cams on my basically stock cobra, good idea?
A. No, it’s a bad idea. Cams are expensive (900), they usually require springs (600) and are a pain to install (800), so they are not a good idea. They don’t add much power on a basically stock cobra and are really a mod to do after you’ve done bolt ons.
Q. Tranny fluid, whats the best?
A. Hard to say. Most people use either GM synchromesh (Pennzoil synchromesh is the same thing but cheaper), some use redline and others use royal purple. The stock fluid is ATF (not mercon V though)
Q. How Do I change my tranny fluid?
A. Jack up the car until it is level front and back. Get a drain pan and find the fill and drain holes. On the t45 they are on the tailshaft housing and the fill and drain are both on the passenger side of the tranny. On the tr3650 the drain is on the bottom, the fill is on the passenger side. MAKE SURE TO LOOSEN THE FILL PLUG FIRST SO YOU KNOW YOU CAN REMOVE IT. So remove the fill plug, then remove the drain plug using a 3/8s ratchet. let it drain for 20 minutes or so and then reinstall the drain plug.
Now using about 3.2 quarts of tranny fluid, get a 3/8th outerdiameter hose and a funnel. Remove the shift knob, the shift boot (pull up from the plastic surround, should come out easy.) don't remove the electrical connections, just let it hang off the side. now, remove the 4 8mm bolts that hold the rubber boot down. pull that off the shifer and then snake the hose down into the fill hole. pour the fluid in, and then reinstall the fill plug. seems complicated but its not.
Q. My engine squeaks when cold?
A. Most likely a belt tensioner pulley bearing. Also possibly an idler pulley bearing (1 on a 99, 2 on an 01). Go to a local bearing shop and have them pop a new NTN 6502 bearing in. should cost about 5 bux and you’re set.
Q. My engine won’t idle/dies when I come to a stop/or revs up when I push the clutch in.
A. 90% of the time this is caused by a dirty or faulty Idle air Control (IAC)motor. This is the silver canister located on the passenger side of the intake right by the throttle body. It is held on by 2 8mm bolts and an electrical connector. To clean, take it off, spray it with brake cleaner and either swish it around or use a q tip to clean it. If that doesn’t work, try replacing it. About $80 at ford, around 60 at parts store. Quality of parts store parts unknown.
Q. My engine runs crappy, low power, and backfiring?
A. Try cleaning the maf. It’s the electrical sensor located right after your air box. It requires a tamper-proof torx bit to remove and electrical cleaner to clean. You can figure out the rest.
Q. What should my fuel pressure be at idle, cruise, and WOT?
A. Fuel pressure is always delta pressure- (manifold pressure/2). So at idle, you should see about 20 inches of vaccum. Delta pressure is 39 psi, so you should see about 30 or so psi at idle. This works for all varying levels of throttle. At WOT or zero vaccum, you should see 39psi of fuel pressure.
Q. What should my oil pressure be?
A. the stock oil pressure gauge is useless. Its an on/off switch that reads 60% pressure over 6 psi and zero below. On an aftermarket gauge, you should see about 90psi at cold start. 25 psi at hot idle, and above 75 at 3000rpm cruise. Ford specs are 20 to 45 psi at 1500rpm.
Q. When on the highway at around 2000rpm and I let off the gas, and then get back on it quickly, i get a clunk, what is that?
A. That is most likely the backlash in the gears. They tend to be a little sloppy in stock form so they can clunk on transition from coast to drive.
Q. What gears should I get for my car?
A. that depends on a few things.
1. How is the car used
2. How is the car set up(NA, spray, boost)
3. traction
4. personal preference.
If you use the car daily, and drive a lot of highway, something like a 4.30 gear might be a bit steep. However, for a drag race car that is barely ever street driven, 3.73s are not enough. these cars are not like a 5.0, they make weak torque down low and most power up high, so you need more gear (especially since they are heavy). So, as a general rule of thumb, if you do just about all highway driving and don't race it, 3.73s or 4.10s are good. If you do street strip stuff, then 4.10s or 4.30s are good. If you do primarily drag racing, 4.30s or 4.56s are the way to go. Keep in mind that with 4.56s you may need to grind the cross pin to get it to fit.
2. The more power you have, the less gear you are likely to need. NA cars need the most gear, centrifugal blown cars need the second most, turbo and nitrous cars need less, and roots blown cars really don't need much because of the massive down low torque. However, its back to personal preference.
3. If your car can't hook, all the gear in the world won't help. So if you want gears and have decent power, don't expect it to hook without suspension work. If you don't want to touch the suspension, adding a ton of gear might not help at the track (at least get some better tires)
4. Personal preference is just that; personal. Some people don't like seeing 2700rpm at a 70mph cruise and for others thats nothing. some don't like shifting after 30 feet out of first gear. Some people don't like worse gas mileage around town that come from gears.
For reference with stock tire diameter and tranny, 70mph with stock gears is about 2100rpm. 70mph with 3.73s is like 2400, 4.10s is like 2650, with 4.30s its like 2790 and with 4.56s its closer to 3k.
1999 Belt Routing
2001 Belt Routing
Blown 99 belt routing
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