Wow , bad luck.
I once had a complete new motor installed in my 500.Drove into quicksand stuff, before I could hit the kill switch it inhaled mudwater and destroyed everything.
Its bad when theres mud in the exhaust!!
If there was just water in there your okay, what concerns me is the dirt. Once dirt was been churned through a motor you really got to look at everything.
There is most certain damage to your piston and rings, hope your cylinder is okay, it could have been scored.Since dirt was drawn through all your bearings in the bottom end are suspect and should be inspected.
If it were my motor I'd pull the whole thing out, take the topend off and use some ATF to thoroughly wash the bottom out, maybe you'll get lucky on this. If you feel anything at all you have to get to the main bearings and connecteing rod bearings for closer inspection and possible replacement.
Nothing worse than replacing the top end just to have your connecting rod bottom go out and gernade your motor.
If I drown a bike I immediately take the filter off and plug out.Check the airbox that is clean, no dirt got past filter, really wipe the area(I always carry a small towel) .Put bike upside down and turn motor over to expel water,sometimes you have to have it up on the back wheel in wheelie position to clear pipe.Wring out filter , clean with some premix and reoil with premix or oil if you have it, plain motor oil will get you buy.Put new plug in,kick.
Better to really go over motor now, I know its a pain but its better than breaking down in the middle of no where in the future.