Well for one the LS won't have the VTEC system wires in the harness, and the 2001 is OBD2B, while the 1996 is OBD2A. I'm not 100% certain of what all of the differences are with that, but i'm pretty sure the plug connections at the ECU are different from A to B.
An obd2a engine bay harness works on an obd2b car, it also has that blue tach wire to the one of the shock tower connectors. Connecting a gsr engine harness to an LS leaves ton of unconnected stuff. But can get you mostly running...
I am currently using an obd2a LS engine bay harness on my 2000 with GSR swap with no issues (plus vtec subharness). I stupidly bought a GSR harness that sat for years in my garage and it was basically disintegrating by the time I did my swap and went back to an LS harness to solve my weird issues I was encountering. Should have kept my original harness even if I would have had to add the blue tach wire
You are right about the ECU side being different though. That is where I am not certain how the VTEC, Knock, and IAB shock tower plugs are wired in...Im guessing directly to the ECU?
Last edited by aw614; 05-29-2019 at 09:35 AM.