I dont' imagine that if the issue lies here that the rotor has gone "bad" so to say, but it very well could be on its way out the door...just like my buddies.
I just read through the thread. It was never made clear. Did you block off your vacuum barbs...i'm assuming you did if you've been able to ride it and if so with what? I've had BAD luck with regular vacuum plugs...they seem to occasionally fly off/expand when heated up. Also is it possible that you've got a vacuum leak that only becomes active after the rubber heats to a certain temp at the carb boots? How do they look? New or old? My 77' with BS38's does not have barbs on the carb boots so i'm curious as to what boots are one yours and if maybe they're losing vacuum when they get hot.
Here's my recommendation...and i've been through this on all 9 of the bikes I own. Isolate the systems of the bike. Igniton, charging, fuel/air delivery. Once you know its not 2 of these, you've likely found where the problem lies. From what we know it doesn't sound like the ignition is bad especially since you have spark. You know you have fuel flow...but we don't know the details of what the fuels system is doing yet. We (I) assume its charging if you can ride all day...but that doesn't mean it's doing it properly. It's not as much work/bullSh*tting around with stuff as you might think. Some simple test should lead you to the culprit. Make sure it's charging and not over/undercharging and then you've pretty much narrowed it down to a fuel delivery issue...assuming all grounds and connections are tight and correct.