Some of the voltage regulators (depends on year and model) derive their ground signal from the mounting ears. Check to see if the mounting ears are clean and tight, if they are there are two bolts under the seat where most of the grounds are attached to the chassis. Make sure those are clean and tight as well. Your issue sounds like a bad ground connection some where. When voltage regulators go bad they often do it intermittently but they go between a charge and no charge state based on heat. They tend to charge fine when their cold but die out after they warm up.

 

I know the feeling. On my '00 it was the stator(s), 3 of them by 57,000 miles. I went aftermarket on the whole system (Compufire 3 phase,) and it's been rock solid since installation (7 years and 100K miles ago.)

 

I replaced the stater with the motorcycle electrics or whatever their name is and it seems to have been working just fine.
I think I've pretty well had it with this bike. I'm looking at the 2016 model now. This one will find it's place up against the side wall of the garage until I decide what to do with it. I doubt I'll ever be able to sell it with all the modification to it. Probably just part it out then junk the remaining parts.

 

I'll be picking up my 2016 RGU this Friday.

 

You're going to love the new RGU. Post a few pictures when you get time.