Hi there - I had a similar problem with my 99 WR400.
When I bought it the same story was told by the previous owner.
It turned out that after a lot of investigations it was the flywheel .............
Readings were all fine on the stator / coil etc.
The magnets had all disintegrated - they were still encased in the thin metal shield but were in hundreds of pieces.
Have you noticed any metallic crap in the oil ? May be worth checking although the fact that they are magnetic could mean that they stick to all the components in your gearbox and sump etc.
Let us know what you find - If I were you I would not risk trying to turn it over too many times before you strip that side off - just in case there's metallic crap in there .....