Have you considered it being the Neutral safety switch? It's about 6 inches above the shifter and has a wire plugged into it. Check that wire for a good connection. Remove the switch (think you'll need a 13mm spark plug socket) clean it up and pop it back on, and push the plug back on, push it well to make sure it's on, you'll feel it find it's seat.

I had a similar issue and just a quick clean up sorted it.

 

my bike has had the same symptons before. it was the regulator rectifier.
its located on the left of tail. i bought a new battery ran fine, stopped the bike and tried to start again it was dead. the regulator converts AC to DC so it can charge the battery. something like that.

 

Did you end up buying a new rectifier? Did that fix it?

 

I hadnt considered or even heard of that. Ill try it and let you know. Its good to know im not the only one with these issues.