All of what Dave has mentioned, plus, make sure your idle on a hot motor is set pretty close to 900rpms. I'd be looking for an air leak, also. The intake manifold to head flanges are often suspect. After 13 years, it really never hurts to remove the manifold, surface the flanges, and reinstall it. As dave mentioned, you may find the manifold in such bad shape replacing becomes a viable option. Even with a new manifold, take the time to surface the flanges, before installing it. Yamaha uses orings and grease on the flange surface to allow it to slip and slide and seal when installing. Many here, use the blue high temp non-hardening sealer like Hylomar. Permatex makes one called Permashield. Don't use a silicon type sealer that can harden. If you use the sealer, instead of grease, just use it on the flange outside of the orings.
If you end up digging in that deep, you may as well replace the needle and seat(float valve) on the carb
, also. Avoid being ham handed, and messing with the float If you do it. If you regularly use something like MMO
or Seafoam in your gas, the inside of the carb will stay in good shape, as far as clean.