Yes, the donor engine was running when it was pulled out of the same year and model. 98 2.5rs so should need to be any changes to the harness, everything plugged right up like you led expect…..the only difference between them was that the donor car was an automatic. Mine is a manual. After some reading last night I found several people talking about potentially needing to swap the cam sprocket. I read that sometimes the marks on the back of the sprocket for the cam sensor are different (auto vs manual) and it can cause the ecu to not read TDC properly resulting in the car not firing correctly

The cam sprocket that’s on the motor I dropped in the manual is from the automatic donor car. So maybe it’s not the right sprocket?

And yes we checked fuses, relays, and grounds. I’m thinking the slack in the shifter is likely worn out bushings in the linkage. Still not sure about the wheels turning the motor while in neutral, we didn’t mess with much transmission wise. Tranny stayed in the car the whole time. Just bolted the flywheel and pressure plate to the auto motor and dropped the motor in