99 and up had IRS suspension not any 94-98 cobras. THe only difference is the Ring and pinion which varies on where you get the rear end from. ANd the fact that cobras had larger better rotors and pads with different mounting brackets for THE SAME CALIPER (as on the GT). So if your getting a brake assembly with the rear, then keep that in mind.
the cobra's have thicker vented rotors with thinner pads/same calipers. the cobra's all came with 3.27:1 gearing. i'm not sure what gears the 94-98gt's came with but the 99up gt's i think come with 3.27 and the 93 5spd had the 3.08 option. i think all the auto's came with 3.27.