OK, so I finished moving the wiring harness today. The bike actually fired up and ran afterwards, so that's a bonus.
Basically what I wanted to do was relocate the fuse junction box and IC ignitor box located at the bottom of this picture. You are looking down on the bike with the seat support being the black piece of metal running across the top of the picture. If I remember correctly, the wiring harness ran around the outside of the seat bracket and behind the two boxes. The goal was to get the boxes moved and any wiring re-routed so it wasn't behind the seat bracket. the loose wires in the middle of the picture will go to the taillight and rear turn signals. Stay tuned for more pictures and details.