I can't believe that I forgot to update this thread. Here's what the wiring harness looked like when I finished it.
ECU side unwrapped.
Middle of the harness bundled together. Note the few splices I did make are staggered, and kept sealed with heat shrink tubing.
Engine side of the harness.
Here's the harness after it has been taped up, and wrapped with silicone tape.
I didn't wrap each connector with silicone tape, as I plan on using wire loom to cover and protect that. All in all, it was about a week and a half worth of work. (A few hours a day, mostly while watching TV at night). It wasn't too hard to repair, but it was very tedious to say the least.
Thanks for everyone who chimed in, and offered advice or help. I don't think I could have done it without you.