The answer is both yeas and no. Let me explain
1. The 1996-2001 GT's and Cobra's have t-45 transmissions (which will bolt right up at the engine side.
2. The Tailshaft is different between 96-98 Cobra's. A 99 Cobra t-45 will fit a 99 gt though. Make sure that you have the same type of speed (mechanical or electronic) sensor/gear.
I am putting a 97 GT t-45 in a 97 Cobra and it has turned into a project...i am changing the tailhousing and speedo gears right now....