I am following along on this build. I did something similar a few years ago and scratch built a Robo War playfield and hand wired it. I think I bought like 4 wiring harnesses total and used a Black Hole harness as the base for it. The Gottlieb harness comes apart in sections and the A3J3 harness is nearly identical on most system 80 machines so it only needed a couple wires swapped around to make it work the rest was not nearly as simple though.
I never even thought about coloring the wires myself, I broke all the harnesses down to primary colors so I have boxes and bags full of wires in my garage now.
If you need anything let me know, I have a set of populated playfields for HH.