I own a 1999 Ford f150, I did an engine and transmission swap. I installed a 5.4l dohc and a 4r100 transmission. The original pcm won't control the transmission, is there a program I can download on a laptop to manipulate the the pats system and install a salvage yard pcm. Or should I just pay a shop to fix my problem?
Because you didn't mention which engine was stock in the vehicle (4.2, 4.6, 5.4 gas or propane), what I can categorically recommend is that you'll need the proper computers applicable for the engine and transmission, and in addition, you'll probably need the applicable wiring harnesses as well.
Also, in swaps of this type, sensors and other necessary components have a way of being damaged quite easily, so perhaps you should be prepared to have a good mechanic with the proper tools and diagnostic computers assist in making it all work.
Sorry I can't be more positive, hope this helps.
I agree with RetOldPro.
You should either go to a Ford dealer or ask an experienced mechanic with proper devices for help.