From everything I've gathered in my search for parts interchangeability, EVERYTHING from the V6 will swap to the '94-'95 GT.
Including the transmission itself.
Aside from the rear axle being a 7.5" vs the GT's 8.8" setup, the two cars are *close* to identical on drivetrain. I've been told that the V6 cars have a slightly "lighter duty" version of the T5 transmission, but running the ACTUAL numbers on them at work, they both come up as the exact same transmission. Long story short, the 3.8L cars use the same base parts as the GT 5.0L.
Pedal assembly, wiring, driveshaft, etc. should be a direct swap for your car. I myself am putting a 5.0L H.O. from a Lincoln Mk VII into my car this winter, and have been toying with the idea of doing a T5 swap as well. I found a donor car ('95 3.8L 'stang) for everything I need, I just don't know if I want to spend quite that much money/labor in doing the swap. I don't plan on racing my car, mostly just planning on keeping it as a daily driver for the nice-weather months.
So, in conclusion, yes. Almost all the V6 parts will swap to your car. The one MAJOR part I know of that won't is the flywheel. You will definitely need to get one for your 5.0L, or it will throw your balance off and ruin your engine. Other parts you should keep in mind are, (not in any particular order of importance, all are needed)
* Transmission
* Pedal assembly
* Clutch master/slave cylinder
* Driveshaft
* Manual transmission EEC (computer)
* Flywheel and new clutch assembly
* Shifter
* Transmission crossmember (I believe they are different, but could be wrong)
* other misc. small parts I have probably forgotten about
If you decide to do the swap, I wish you the best of luck. It shouldn't be too difficult, but will most likely be time consuming, and possibly expensive. Keep us posted on your progress, though.