Bought a aftermarket pcm and installed it but.

Bought a aftermarket pcm and installed it but still didn't fix problem so brought the truck to a ford shop and had them look at it and they said that it most likely was a bad relay and that one of the two keys were bad and that they didn't know which one it was and that they couldn't get the computer to work correctly with the new pcm or relearn the keys - is there anyway to figure out which key is bad and is there something else that we can do to diagnose what could be the problem so far I am down $250 for the aftermarket pcm and they said that we are looking at least $496 for the relay and bad key