Hi Mike, I would suspect the brushes and/or dirty commutator, I am pretty (but not 100%) sure the dvr2 needs to see a voltage on “D” before it will start giving power to the field coil. This voltage results from “residual magnetism” in the field core when the engine is running. If there is no residual magnetism, or it is the wrong polarity, or the brushes have enough resistance the dvr2 won’t start giving power to the field coil, hence no charging.
It was many years ago but I had a similar issue where I would go about 400 miles and charging would stop, cleaning the commutator fixed this but the issue would return, new brushes fixed the issue more permanently, I assume the old ones were soft, and made the commutator get dirty.
I found the problem by running the bike with D+F connected when it was in the not charging state, it did not “self generate” and power a bulb, but briefly applying a voltage to two connected wires started it generating, and it kept generating, so the issue was it did not “self start” from residual magnetism.
Your bike does “self start” by the sound of it, but maybe it is not doing that consistently?
There must be a test you could do whilst the dvr2 is connected, to emulate a “self start” eg apply a voltage to the field coil or armature, but not damage the dvr2.