Condenser failure conjectures
This may or may not be helpful.
On my older /2, the condenser went bad, and the way it showed up was after an hour or so of riding, it apparently would get too hot. The engine just quit. I remember walking (pushing) my bike home (I wouldn't have dared leaving it where it stopped and picking up later and this was before cell phones) about 3 miles of uphill, and coasted downhill.
I purchased a new condenser, cleaned the points, and it never quit again.
There are others who may know more perfectly than I, but a condenser is a mini-capacitor. It stores up "small" electricity over a period of time and when circuit is broken (points break) it surges all that stored electricity in one large flash to the coils which in turn, produce the spark.
I am wondering if there isn't some sort of ignition short or arcing (either in or around the coils causing the charging system to "see" a surge in electrical usage (causing the charging light to flicker or come on) and the short causes intermittent spark misfiring. I also saw something similar in my son't Volkswagon Golf. It had a slit in one of the spark plug wires. It would idle and run fine until under load (heavier acceleration) which would then cause the electricity to "find" an easier path of resistance. I can imagine if this were bad enough on a 4-cyl. engine (1 in 4 ratio) it would show up much worse on a 2 cyl. engine where 1/2 the power would be interupted.
I recently purchased a 78 R100/7, and it has DYNA 3 spark system on it. Seems to work perfectly, though I almost always distrust electronic anything on a transportation vehicle.