Ok so the Yamaha tech is on holidays now of course, so i found a guy in another small workshop who said he thought he knew what the problem was... he didn't so we went through a lot of trial and error. Found some corroded connectors but nothing that would fix the problem. The only real symptom is the earth wire from the regulator heating up... although when this first happened, the ABS light came on and I got an error 46 on the dash.
We cleaned connections and the earth on the engine, no change, changed the battery... starting to seem like a problem with the ABS pump. $1000 for one of those.
Talking to Yamaha tomorrow to see if there is a definitive test.