What about where the intake manifold attaches to the heads? That's a notorious place for Roadies to leak air. Especially as they age, and people are removing and replacing the carb
. If its never been off the bike, it would be worth it, just to surface the flanges, and reseal it. Although Yamaha simply uses grease to seal the flanges(so they can move a bit as their being tightened), many of us have gone to Hylomar, or the Permatex Permashield on the edges of the flanges outside of the orings.
You can check for exhaust leaks at the heads, with an incense stick or a lit cig. If there is a leak there somewhere, the ember will glow with the air blowing on it.
Make sure the idle is set to about 900rpms, also. Do it when the bike is hot after a ride, and then leave it be.