Yes don't try to swap out motors, even with all the changes you would have a vehicle that may be viewed as "tampered with" as far as smog equipment/changes made (trips to DMV to get it authorized).
If the check engine light is on there should be codes stored in the computer either the computer is faulty or the scan tool used is incapable of reading the codes stored. We have three scan tools at my work some times one tool works better than an other with different models. A professional grade scan tool can read codes, pending codes, key sensor live data and Modes 6 information.