Ok guys, still having issues. I did the ringfree treatment both in the ports and throught the carb. Blew all kinds of black soot out of only the rear cylinder. Ran great for two tanks of gas now it's back. Won't idle, stalls,ect. Yamaha offered me $200 toward the valve guide ream job. That will cover the bill since I'll pull the head head myself. However this is not a garantee. My dealer, which I worked at did 3 of these and one svs came back...........he finally bought a harley....lol. I just don't know what to do. My bike is set up very lean 167.5, 32.5, and 2 turns out. Why do I still have carbon building in the rear cyl? I seen another post where the ais plug came out of one's bike. I have not checked this but.............who knows. I don't even remember plugging a line when I pulled my ais?

Should I ream the valves or just ebay the bike. Prob there is I have $18,000 in it and nada might be $8,000.........oooops!

Thanks everyone for your help and efforts, I wish yamaha were as helpfull as you all have been! They won't even aknowlege there is a problem. Sad, I had more yamaha's thank I could count on my fingers and toes.

solan,
there has to be some fuel leaking into the carb someplace... all the numbers seem good, lean jets and pilot. I would have to check float level and the choke circuit to be sure not letting fuel in...
I would also keep running some sort of fuel additive like ring free in normal amounts (not shock)for a little while till all seems on the good side than go a couple tanks without, and again a tank with.
My 06' knock on wood seems good but I still use MMO every few tanks just for protection and I run it up to the rev limiter everyday at least once.

JTSr - your altitude, Musky is right you might want to rejet and if you have pipes you will probably be doing the air filter change soon anyway..