Patrick,
Since you have 1,000 hours on it, that is at least carbon build up and possibly (hope not) the exhaust corrosion issue we've all heard about.
If it were my engine - I'd do 2 things (others on this site may have other ideas):
Number 1 - add a shock treatment of Ring Free or Sea Foam to your fuel. The best way to do this is to remove your water separator filter (big blue 10 micron one), drain out the gas, fill it with a pint of Sea Foam or Ring Free, then re-install it (I'd use a NEW filter).
Number 2 - if you do have the exhaust corrosion thing going on, you will eventually, and gradually, hear an over heat alarm go off at some point. If, when, this happens, you will need to limp home, haul the boat and have a guy diagnose it. Then buy the Yamaha kit to fix it (around $1,000 I think). Then find some Yamaha Technician or shop who has done it before. It's not the end of the world if this is the case - just something you can do in the off season which ain't that far away. Once done, your engine will out last you!
My bet is it's simply a bit of carbon build up which the Sea Foam or RF will clear up. You might also change your plugs AFTER you do the shock treatment as they will surely be ugly after the carbon burn off is complete.
Good luck!