First thing, you need to decide what is most important and where you plan on taking the car and how much you want to spend. I agree with above, wheels are a great investment. They help looks an performance, but to me a stock GT sits to high so my first Mod would be lowering springs, or even better a matching suspension "Kit". Your stock Rims and tires will get you by until its time to invest on new tires, then but a rim/ tire package.
Performance... nothing beats a tuner! Axle backs, sounds great, but do little for performance... but did I mention, they sound great! If you decide on a tuner go with AM SCT with tunes for life, that way any mods you do in the future will be easy to change the tune to match. Add an Air Raid CAI to the tuner while you are at it. Again, like exhaust there is very little improvement on Performance, but its a good combo.
Either way, make it you own! That's part of having a Mustang. As long as it meats your ideas... its a good mod! Good luck!
2011 Roush Stage 2 Convertible Race Red with painted gloss black stripes, Charcoal Interior-Roush # 11-0306
Bama Tuned, Roush Front and Rear Brake Kit, Roush Exhaust with Square tips, 20" wheels, Roush seating with Red stitching
Roush Billet Grille matching lower 3 piece, Matte Black side and top stripes, White Face Gauge cluster, Convertible Light Bar Purchased 27Dec2010
Dyno'd 401 HP/ 390 Ft lbs at the wheels