cavalier PCM and crank re-learn procedure

My friend was having problems with his 97 cavalier engine, so he replaced the whole thing, brand new. But he was getting no fuel to his injectors and the car wouldn't start. So he messed with the wires and all sorts of things until he thinks he messed up the PCM. So he got a brand new PCM. He installed it and the engine still won't run. His theft security light (or something like that) comes on and won't go off and when he turns his car to auxillary his lights come on suddenly. His PCM came with instructions saying that he may need to do a crankshaft re-learn procedure, but the instructions on how to do that may as well have been written in latin. I think he said that his check engine light doesn't even come on. What 's wrong with this car?!