My comments are somewhat after the event so you may have sorted it by now, but:
Regarding the crank not running true, if you remove the side cover and start the motor and look straight on at the end of the cam I would have thought that if the crankshaft was running so out of true as to be causing your problem, then you would be able to see the generator slip ring actually running out of true and also see carbon brushes jiggling about backwards and forwards in the holder.
I would also imagine that if the shaft was bent and the rotor was running out of true, it would cause a serious vibration and as there is not much clearance between the rotor and stator coils, there might be a sign of rubbing between the two.
I just wonder if there is some damage right at the end of the shaft where the points cam locates due to a previous owner riving off the rotor with the wrong extractor tool. If so then could it be that the cam is not seating properly?
Final thought, are the engine main bearings OK and not really worn on that side which might enable the shaft to flail about a bit!
Other than that, I’m stumped!