I took the gas tank off you my surprise were two wires brown and pink that weren’t connected to anything. Additionally there is a hole where it appears something went there. I have a manual but the wiring diagrams and pictures aren’t very clear, any one have any idea?

Horn

I guess few more words would be helpful.  Those wires should go to horn.  Brown is + with key on and pink grounds when you press horn button.

As you probably know, the horn does not attach to that bracket...  I think bracket might be for turn signal flasher as I can see someone has plugged brown and brown/white together which is not correct.  Brown powers flasher and brown/white comes out of flasher to turn signal switch.

+1 to horn.

I don't have a HT1, but on most (all?) Yams that I've owned, the horn mounts somewhere around where the two "arms" of the frame meet, below the headstock.

Folks often plug the brown and brown/white wires into each other when they remove the flasher relay, just to keep them out of the way. 

Flasher bracket for Ht1