you need to keep your harness thats in your car right now the one in the engine bay has nothing to do with the ecu the ecu is running from the inside harness. your clutch will work in it no prob. find someone to trade you ecu's actually just get yours chipped for a better fuell map no need to change your car to obd2 your ecu will run that motor just fine but gettin it chipped would be the best idea. you would have to change the whole wiring of the car to do obd2 not a good idea.
chip the ecu
use your wiring harness off your motor