What is the case learn procedure? Is that a certain task/parameter that one should do when putting a new engine in a car? My uncle built the engine, I know a ton about cars but I don't really know exactly what HE did to get this thing running.

A case learn is an optimization for the pcm to know where TDC is located. It can only be performed (to my knowledge) on a running engine.

I don't know if that was done, but the motor does run, and I don't have any check engine lights.