Thank you Mark T! I drew it out so I know exactly what I will be looking at when I get home. THANKS AGAIN! 

Thanks everyone who responded to my post, and especially Mark T. Hooked up the battery correctly, but still nothing. But I knew I had several bad connections inside the headlight. I ended up cutting out the multiple jumped male/female bullet terminals and hard soldering them instead with shrink sleeving to protect against shorting.
I now have a horn, turn signals and brake lights. YAY!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Congratulations on the progress!

Thanks Mark! Now waiting on parts from Yamaha (clutch shaft seal, oil pump parts etc..) to continue further,