So we have a CANADIAN 1999 SI coupe. It was auto and we are doing a manual swap. We got the P2P-C12 ecu which is the obd2B manual ecu for this car.

now the question. The one plug on the auto harness is said to be for the auto trans. Is it safe to say that we can undo the loom and remove all those wires? Or can we just cut all the auto plugs off and re tape the harness?

 

I wouldn't cut anything at the ECU end... just leave the plug dangling near the ECU. If you want to clip off all of the auto trans plugs in the engine bay, you certainly could do that to help clean things up. I would recommend individually terminating each wire to eliminate any chance of shorting or arcing by any of the cut wires. Then re-tape the loom and you should be good to go.