I'm not a fan of wiring. never have been. Ive taken your approach to it many-a-times, usually with lack luster results (read: some bad connections or accidental grounds). Ive finally become soo fed up with shit not working and taking hours and hours to trouble shoot and ohm things out and "see if it works now. how 'bout now? now?..." I know taking apart the whole wiring harness is a daunting task when looking at it from any starting point, but hear me out. If you take that wiring diagram and remove all the things youre going to leave off the bike, like those two lockout switches, maybe the idiot lights, the two sets of empty accessory leads, etc. you could have close to half the number of wires left. Now take that new diagram and wire the bike from that. Use the right color wires from the harness you just removed and solder all the joints. Yes, it sounds like a pain in the balls, but Its only a solid 8 hrs of work, and youre planning to spend 6 hrs to on it already in the hopes that you fix current problems. Its less time, effort and frustration in the long run. Ive done two kawi 750's this way (twins though). They were plagued with electrical problems initially, and now everything works when I want it to. and I'm not good at wiring.
just my recommendation.
and from the looks of it, this bike is in much better condition than mine was when I got it. you got this. keep the pics and progress coming