It's called the head, bud. 2T's don't suffer the valve disea...err have valves and cams and suchI have a feeling he may have flooded out the carb or even the engine it's self if the water got into the air intake. You should take off the carb bowl and see if there's any water in it, if not then take off the cam cap I think its called. It's the cap that leads to the top of the engine. Check for any water in there. If there is water in it, then drain it out of the motor or suck it out with a shop vac. Then leave it off for the rest to evaporate. Once it's dried out then check all the engine seals for cracks. If they are all good re grease them and put them back. If the seals are all good then you must of got water in your intake. That's no big deal. If any seals are bad replace them.
I would be very cautious about turning over your engine, if any gritty water got into the intake it could be in the cylinder, so you should check everything in the order that things happen on the bike...It's called the head, bud. 2T's don't suffer the valve disea...err have valves and cams and such