Id do the exhaust and tuner first. You could do the Pypes "The Beast" X Pipe and catback kit on American Muscle for about $550. The X Pipe will make the car sound really nice with the catback, and youll definatley feel a power differance.
Pypes THE BEAST Exhaust System (99-04 GT) at AmericanMuscle.com - Free Shipping!
As far as a Tuner, Id go SCT. I have a Diablo Tuner for my GT, and my dad has an SCT for his Mach 1, the SCT is a lot better.
Then Id do gears. Could do 3.73s if you want to cruise without hitting higher RPMs (not to much of a differance than 4.10s) and if you plan on going Supercharger, Nitrous or Turbo.
I have 4.10s and there awsome, car felt 10x better and a lot faster after they were installed. I can chirp 4th gear pretty good with them.
Hopefully this helped, good luck man.
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2003 Mustang GT Redfire
1/4 Mile - 13.408 @ 103.10mph | 60 Foot - 1.934
261rwhp & 284rwtq Tuned by Mike Dez @ Dez Racing
4.10's, SLP LM 1 Catback, Mac o/r Prochamber, K&N FIPK II CAI(painted red), MAC 70mm TB, C&L Plenum, Diablo Predator Tune, B&M Short Throw Shifter, Mach 1 Chin Spoiler, Mach 1 Grill Delete
Next Mods - Saving for a Procharger :)