If you're getting an assortment of codes thrown, it's probably a systemic fault (as suggested above) rather than anything wrong with the harness itself or any of the errors indicated. My experience with this a few years back (also on a '99 OBW, EJ25D) was that after doing a motor swap the transmission was acting really wonky e.g. the 3-4 shift points were drifting all over the place. I read the xmission controller codes, and they were telling me that there was a problem with communication between it and the ECU. So I got out the 'scope and poked around and everything looked okay, and someone on one of the other fora suggested a ground fault, and I kinda thought it a crap suggestion, but went through the TSM to spot all the under-hood grounds, and although they looked okay I reterminated all of them anyway, and the problem persisted. Ultimately, I settled on the ground not indicated in the TSM diagrams - the one on top of the intake manifold next to the coil pack. Captain Dumb@$$ had failed to tighten that one down after the motor swap. Did so and everything got better.
So it's easy to say "look for bad grounds", but there's nothing like one for making crazy errors appear all over the place. That's where I'd start.