Yeah, seems like it's not getting enough "fire in the hole." Sounds like it lasts for just a short time, then once the battery/charging system fails, that's it.

Also, we now know the previous owner was trying to diagnose this as well, given his hand-written notes in the service manual. I would go down the road of checking all things electrical, first, before the fuel system, based on what's been written so far.
My first bike was an 10 year-old 1980 Yamaha 400 Special. When I got it, it had a gummed-up fuel system from sitting too long but it still ran if you messed with the choke and throttle enough. It's hard for me to imagine that the fuel system is so clogged as to keep any fuel at all from entering the carb. I guess it's possible, but from the decription about how the lights are behaving, it seems more like an electrical gremlin, at least to me.
