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Stator.
Finally found the issue. Took stator off (easy, compared to the oil filter gauze, which is a total nightmare of a job) looked fine, no really bad spots but a few obviously 'lightly toasted' pieces of insulation on the coils. Put back on and then took a Vac reading between them with motor running. At idle got 7v/15v/15v, and through the rev range the same, the two healthy phases returning upto 70Vac, the duff one never getting above 15Vac. So thats whats causing it! Although all three phases return very similar resistances, 2.6ohm each, thats over the max they are meant to be regardless. So through both measurements, the stator is toast.
Thankfully didn't end up spending mechanic time getting it found and learnt a thing about charging systems, so all good really, apart from bank balance, fecking £50 for a china part, £150-170 for a yamaha, but made in china in the same factory part. Gonna chance the china part
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BrickMan
coppiThat
That diagram has helped me diagnose lots of problem bikes.