When you swapped motors, did you also swap all of the intake manifold stuff - e.g. throttle body, etc? How about all of the sensors, are they new, or at least different?
If so, I would start with sensor wiring. Check connectors on the engine bay side, you may have to disassemble, restrip, and resolder some of them. Hopefully it's not an issue deep in the harness.....
Nothing wrong with trying a different ECU, shouldn't cost anything to try.
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