To everyone who responded, thank you. To those who were trying to figure this out, thank you.
The problem is fixed. Turns out it was the emergency brake cable. The night this happen not only did I lose the guts in the exhaust I must have hit a rock or something and bent the rear guard for the brakes. The guard bent the adjuster up for the emergency brake, this in turn engaged it. If anyone else is having trouble with their quad not running right, check this first. In my opinion this is a very stupid design on yamaha's part. stupid,stupid,stupid this can not be said enough.
Thanks again for the help.