1993 Ford F-150 pcm swap

I bought this truck knowing someone had put a after market tuner module in it. The truck was not running right so I decided to take this out and put in a new pcm to make everything back to factory settings. When I installed the new pcm the truck would not start. After much research I found that the pcm that was in the truck when I bought it was out of a 93 mustang 5.0L. The issue with this pcm is it will not let the transmission function properly. My question is what did they install to get the mustang pcm to work, so I know what I have to change to make factory pcm work?