First of all, I'll bet you my car that the block didn't crack. You probably only had an upper intake failure that could have been repaired for about $200 US.
Secondly, please put "95se" in your signature. It'll help us to help you.
Thirdly, there MIGHT be some sensor problems and differences between 95 and 96, but I wouldn't expect it to be major. You need to get all the sensors inspected....disconnect and reconnect anything you can, and look for damaged wiring harnesses that could have happened during pulling/installing the replacement motor.
Your mechanic can't read the codes because he probably doesn't have the proper reader. The 95 is a hybrid obd1/obd2 computer. It'* not obd2.
And I'm amazed at his compression checking skills as well.