They can go bad. I know they can just loose their minds per say and need to be re-flashed also.
You pretty much have to stick with the same DTC type as far as I know. But I could be wrong about that. The California PCMs are a different animal. The Super Duty PCM is different than ours too. They can be made to function in these rigs. But unless you were going with a 4R100 in place a E40D I don't see the advantage.
Your PCM code can be read on the driver side of it if you have good eyes. I used a inspection mirror.