the OBD2 engine harness will plug into your shock tower connectors to your chassis harness. You will have to run wires from the shock tower plugs to the ecu for:

4-wire O2, vtec, knock sensor, (maybe vtec oil press, some jdm engines have this, some don't), (maybe do a 2-3 wire IACV conversion)

this is much LESS of a wiring nightmare than trying to get that thrid ecu plug on the OBD2 chassis harness wired into your chassis.

-PHiZ