Unless upgraded, 6v system is standard.

No power to the headlight yellow wire and green wire until engine running.

To test that the headlight bulb isn't blown, you could wire your headlight direct to the (6v!) battery with some lengths of spare wire. These bikes weren't initially fitted with voltage regulators so, after time and other electrical components being past their optimum, headlight bulbs blew. Yamaha issued a Service Bulletin to advise on the fitting of a regulator and a link to this is attached.

Vintage Yamaha Enduro Fans - Service Bulletin #M5-084 re Voltage Regulators (yamaha-enduros.com)

Thanks, someone did wire a rectifier at the headlight. I did wire the headlight direct and it’s working. Maybe put everything together and give it a test run. Our local motorcycle mechanics didn’t even want to touch this two stroke bike so I’m on my own.

Sincere apologies for being picky, and for the avoidance of doubt, but it's a voltage regulator that should be fitted there - the bike was fitted with a rectifier as standard and this is located on the frame, under the tank. Hopefully it's just terminology confusion. 

Correct, I seen the factory rectifier on the frame. Someone wired an additional rectifier into the headlight circuit and located it in the headlight bucket. Sounds like I may need to remove the second rectifier and add the regulator Yamaha recommended? 

I have had great success adding the rectifier to the small Hondas, I’m not an experienced mechanic so……

I'd say yes to that.

Going off on a complete tangent, is yours a genuine US bike, or might it have been brought back from Japan by a forces person? The reason I ask is that these imported bikes, referred to as JDM bikes, had a big red light that came on if a certain speed (55mph I think) was exceeded. Linked to this warning light was what looked like a rectifier/fuse type thingy that was located in the headlight bucket.