I had something very similar on my CB650. only that 2 cylinders went out. If I read you correctly you have a dyna ignition. Does it have impulsators as pick up, not the standard points? If yes, then it's one of them. If not do another test. Start bike from cold and don't drive it, just let it heat up on idle. If it happens again, then it's temp related issue, and the means 99% electronics ignition system somewhere. Good luck in searching for it. I'm positive it's some heating up ignition component (may be a connection somewhere on ignition too).