There is a green wire with a yellow stripe with a male connector which comes out the end of the wiring harness on the headlight end of the harness, I see the wire down at the the rear brake stop switch on the bike and wiring diagram, but I don't  see where to connect it at the headight end, I don't see a green wire with a yellow stripe coming out of the main switch or the handlebar switches headlight or gauges. 

You don't say what bike but green with yellow strip usually is front brake light switch on front brake lever. Connects in headlight bucket area to main harness. Then that wire runs down to rear brake switch and joins the  yellow wire at the bullet connector. 

DT 3. I'll look again for the connection

Should be a single wire coming out of main harness. There should be a brown wire too. Both connect to front brake light switch.

The terminal on the end of the green/yellow wire coming from the main loom in the headlight shell should be a female bullet. Green/yellow and brown wires from the front brake light switch are both male (see link).

FRONT STOP SWITCH ASSY for Yamaha - order at CMSNL

Thanks to you both. I found the problem, the brake lever on this bike does not have the brake stop switch.