Are those 4 windings lighting/charging coils, or dedicated for feeding the CDI box? If they are lighting/charging (which I doubt), then the reg/rect may be causing it.
Unfortunately, I suspect it may be dodgy engineering and quality.
I have a VAPE in my RD350, which has worked flawlessly for at least 6-7 years now. VAPE ignition and alternator systems have a very good reputation, Hugh's does not quite have that.....