Need help with my 87 4.0 cherokke

I just put a rebuilt motor in a Jeep and this thing won’t run right at all. I can’t really explain how awful it run but it runs like crap. Almost every thing on it is new. It sounds like it had a bad rod knock but the oil is clean. I replaced the pcm and it acted like it wanted to relearn its firing order but doesn’t quite get it. Any help would be appreciated