A new off road x or h pipe (<$200), pulleys(<$200), throttle body(<$200-$250), gears {won't actually increase hp or tq but it sure feels like it}(<$500 installed), nitrous($600 plus installation). Thats pretty much your options for what you want to spend.
Absolutely the most bang-for-the-buck are gears. 4.10 or 4.30 for a DOHC Cobra are recommended (some swear by 4.56s, as well). I'd follow that with exhaust and then suspension upgrades to keep the power to the tarmac...
Save the money and put it towards the 99+ head and intake swap. That will get you an awesome HP increase. Due to the flat top pistons in the 96-98s your compression will be slightly more than the 2001 cars, thus generating more HP than the 2001s.
Here is a link to Sean Hylands package combos. CLICK ME!
That's not to say you couldn't find a wrecked 99+ GT and get the heads and intakes cheaper. Then all you'd need would be the install kit ;-)
One of my Buddies did the 99+ head and intake swap on his 97 GT and I could not believe the power increase!! You could feel the power right off the bat!!! I agree with Alex_96Cobra and GR8WHITE!!!!!!
With that much of a swing in compression (from 9:1 to around 10.5:1) you can't help but make better power and torque through the whole range. I'm looking into the stage 3 package. That should flow just fine with a turbo ;-)