After battling with my wiring harness for almost 2 hours, I finally decoded the mess. Now, my bike has fully functioning signals, headlight, brake/taillight, gauge lights and warning lights.
My color wire diagram isn't completely correct but using that and the b/w diagram from the manual, I finally figured it out.
When I initially started checking into the harness, I found bare and broken wires, connections to nothing, wires spliced and very lazy tape jobs. I finally had to unwrap the whole harness and separate all the runs. Now, I need to find some dry vinyl tape and re-wrap the harness. I borrowed a label maker and every connection is going to get a letter code so this mess never happens again.
One step closer.