I own a 94 V6 and a 95 GT, and I've torn most of each car apart at one time or another. I'm also swapping a 95 Cobra engine into my V6, so I'm pretty sure I know most of the differences. Of course, if I miss anything or get it wrong let me know.
The 94-95 model years shared a lot of common parts between the V6, GT and Cobra. Beyond what's stated below, most everything is shared between the V6 and GT.
The obvious different parts are, as already stated: engine, tranny, rear axle. The computer and exhaust are different. The driveshaft is the same, actually. Also different are the instrument cluster and the seats; the 95 Cobra R had the V6 seats. GT's had fog lights, but the V6 is wired for them. If you swap the fog lights with brackets, the fog light switch and a part in the engine fuse box (I forget it's name right now), you have working fog lights on a V6. Rear bumper is different (V6 and Cobra say MUSTANG). Badging on the fenders is different (duh).
I believe most of the engine bay is different between the V6 and the GT. The radiator and A/C condenser are the same, but the A/C lines are different. Smog equipment is also different.
The k-member and almost the entire
suspension is shared between the V6 and GT. I presume the GT has stiffer springs up front for the extra weight, rather than having progressive-rate springs like most of the aftermarket replacements. You also have the quad shocks on the rear axle on the GT.
Brakes are identical between the V6 and GT. However, they have a different hard brake line running from the front passenger's side all the way to the rear. The V6's line mounts on the right side (where the GT's right exhaust pipe would be), the GT mounts in the center. The connector that joins this hard line to the flexible hose leading to the axle is different. The hard lines on the axle are different.
All the interior and exterior body panels exchange between the V6 and GT, with the exception of the rear bumper. The V6 did not normally come with a spoiler, though I believe it was a dealer option.
The dashboard assemblies are identical, including the wiring. The plug near your right leg is for the V6's OBDII system, and is useless for the GT and Cobra.
I can't think of anything else. If I haven't listed it, it's probably shared between the V6 and GT.
