Great write up. On my 98 GT I run a 2001 Cobra block, forged rotating assembly, dished JC racing pistons, and upgraded to the 2004 Eaton/Terminator top end. Up until now I ran 1999 Navi heads and they produced at high RPMs and 500 rwhp but lost a spring and tapped an intake valve on #8 when getting on it last Fall. Upon disassembly I found that the intake valves in each cylinder closer to the rear were all caked with carbon, while the ones closer to the front were much cleaner, confirming what he says above re air flow. But what I would add is that some easy work with a die grinder on the intake ports of the 5.4 heads will allow you to fit any intake, including a stock Eaton blower. I did it just fine, although I also had to grind off the knock sensor towers you find on the 01 block. But after a futile search for R heads, I'm going with the stock 2004 Cobra/Aviator/Mach DB (casting number) series heads. (Note that it is not hard to find someone who takes them out of an Aviator and thinks they are nothing special - got a mint set for $500.) Better coolant flow and I'm putting the rear bridge mod in too. (The head nuts on 6, 7 and 8 on my Navi heads came off very tough, proving the cooling issue on the driver's side head. It's probably also no coincidence that I lost a spring/tapped a valve on 8.) Heads and plenum are being ported/polished as we speak at Eastwood's in CT with a 3 angle valve job. Porting the underbelly of the Eaton blower myself. Comp cams, degreeable cam gears, beehive springs and retainers, and MAC TF9902 long tubes and matching catless x-pipe. Keeping my magna flow single chamber catbacks Degee the cams, a tune and hopefully we can reach 575 rwhp. I'll let you know what it dynos at.
https://www.svtperformance.com/threads/difference-in-2001-cobra-heads.745711/
https://www.svtperformance.com/threads/difference-in-2001-cobra-heads.745711/
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