Very broad question.
The T5 from the 94-95 GT and 94-98 V6 is a direct bolt in. The T5 from the 99-04 V6 will require changing from a electronic speedo gear(on the tail of the trans.) to a mechanical gear. Clutch and flywheels are different between V8 and V6. The T45 from the 96-98 4.6's is the same.
The V6 engine from 96-98 is the same. There are a few minor diferences to the 98. The 94-95 is also very similar. The 4.6 is the same between 96-98.
The 94-95 uses a AODE automatic transmisson. The 96-04 uses a 4R70W auto transmisson. This is for both V6 and V8.
The biggest diference is that any transmisson bellhousing for a 4.6 will not bolt up to a V6. We have the same bolt pattern as a 5.0.
I'm sure I missed some stuff. What specifically were you looking for???