The 95 GT tranny is a little longer. I believe its the input shaft and bellhousing thats different. When i put an older t-5 in my old 1995 GT i had to get a drive shaft spacer because it was shorter.
Using the 94-95 trans in your car, you'll need the 94-95 specific bellhousing and clutch fork. The input shaft is 5/8" longer on the 5.0 SN95 cars, so the transmission and bellhousing are specific to those years.