I have the same situation and I finally came to the conclusion that it isnt worth the effort. My dad and I own a 95 v6 which blew a head gasket. Long story short, the motor ended up being destyoed in the process and so a debate ensued as to wether or not to make the swap or just buy a GT. In the end my wife and I decided to buy a GT (we are currently looking for one - not sure of specific year yet) because there is so much that must be changed over.
The 5 speed is the same tranny (might be different gear ratios, but same tranny). The ECU, wiring harness, sensors, instument cluster (i have been told the speedo is a different ratio in the GT), front
suspension, all the engine accessories must be changed. the rear end is different and it would appear that it can remain unchanged for a period but the 7.5" rear end is very weak and if you make any mods to the 5.0 then you must upgrade to an 8.8". Plus you need to change the bell housing.
I have been given quotes anywhere from 5-10 thousand for the swap depending on the shop. We started looking at how much a 95 GT would run and they are selling for 4500-6000 in my area (San Diego) so it really isnt worth it in my opinion.
But if you do decide to do it, everyone I have spoken with who has done it has said find a junkyard 5.0 of the same year and tranny setup and just use it as a donor car otherwise you will have issues.
Hope that helps