General rule for swaps involving similar engines, use the wiring harness that came with the PCM/ECM you are using. Usually, that's the one with the car, not the one on the "new" engine.I used the harness that was on the donor engine. Should I have used my old harness?
If you run into differences in connectors, then further research is needed. Often swapping sensors or parts from the original engine onto the donor engine will work.
Finally, a new "tune" for the original computer might be needed to take full advantage of the upgrade.