First mods to do on a 2004 GT.

[91LX2Bfast]

Ford is out of line right now concerning the voiding of warranty's. So if you want to keep your warranty, you have to mod accordingly.
Going along with Blake, I'd say first get an aftermarket shifter. If you have to take your car in for warranty work, and shifter is something that can be swapped back to stock very easily.
You are also pretty safe to do exhaust mods.
Gears are the best bang for the buck, but thats probably going to get your warranty voided.
Heck, Ford has voided several SVT Lightning warranty's because the "correct" weight oil was not run. I don't know about you, but I would not run the suggested 5W20 in that motor either.
K&N's are even off limits now because dumbasses have been over oiling them, which in turn gets oil on the filament of the MAF, which can mess up the reading and lean out the motor blowing it. But you don't need a K&N anyway. The paper cone filter (when clean) flows plenty of air.

So before we get too far into this: Do you care about your warranty?