he took the bike for a ride without the exhaust on the bike

It might be a good time to check the valves

 

Just a little FYI:
Never ever run a motor without a filter...the intake creates a vacuum that sucks in whatever it can. This includes dust and metal and road debris...pretty much the worst thing you can do to your engine.

Also, the best way to clean a cylinder out would be to pull start the quad without a spark plug. Never start an engine with water in the cylinders. This is the best way to force water into your crankcase and at the same time force oil off of metal surfaces. Pull start the engine a couple times and you'll get the water out.

Matt

 

I think in my opinion that use should if you deside to diy take and soak the carb in gas or chemdip etc. to get all the water out. Also take the spark plug out and turn the engine over a few times to shoot the water out of the cylinder pour some gas in the spark plug hole into the cylinder and repeat until there no water left in the cylinder. After you do this put all the parts back like it was carb spark plug etc. Oh and drain all the oil, change it until the oil has no water in it it will be a white milky color but change it till you don't see any of that just oil and while each time you do this turn the engine over a few times to move all the new oil in all the internal parts so all water is gone. And I think that's about all the obvious things to do.