I saw a similar problem on a cat once, never on a yamaha, but you never know? What his turned out to be was a case gasket that was old and cracked and it allowed air to get in on that side causing the lean condition. Once he replaced the gasket, the problem was solved. There should be a way to test for that with vacum or something? However, I'm not the guy to ask and could simply be blowing smoke out of rear, some of these other fellas here like Opsled and Yammie God are very knowledgeable and could maybe tell you what the problem is and where to look. Maybe try a new post asking that question and see what they come with?
Good luck, mine were all drop dead reliable. The only one I ever burned down was the GPX, but that was when I was racing it and had her pushed to the edge. Sometimes I'd melt three pistons a weekend!