I would try to keep the water line about 5 inches or more below the snorkel tube coming off the airbox. Water won't do anything to the other components as long as everything is working properly. If you ride though deep water it's important to lubricate the moving parts after a ride though, because water can push out the lubricants and cause rapid wear.

The reason to keep the water out of the exhaust is that if the engine shuts off and allows water to flow up the pipe, it can either get into the engine if the exhaust valve is open, or restrict the exhaust flow and prevent the quad from restarting.

I don't know much about automatics, but I think the main problem with water getting into the drive belts is slippage and excessive wear.

 

slipping is putting it bluntly.... if you get water in the houseing the bike will run the belt will turn when you press on the trotle, but wheels will not spin. if your not near a place you can properly clean and take the houseing apart a good methid for fixing the slip is to let the engin run play with throttle untill you can move a little bit then cause as much dust as posible. the dust will cause the water to dry . i would sugest that you clean her good thow when you get home .. one thing that will help is to snuckle the dang thing . one othere cheap thing to do is to go too lows and get some sylicon and put it around the caseing itself, then put the screws back on and boom it's sealed . to get housing opened agen you need tocut sylicon with U knife and it will come off.

 

The bottom of the seat is as high as i would go. That is about the same hieght as the top of the air cleaner, and if you get water in the belt housing all you have to do is pull the housing plug out tip quad to that side and drain out the water.Start the quad and let it idle for acouple of min.The belt will dry out and you will be able to move again. Remember when belt is wet quad will act like it is in nutrial. Do not keep trying to rev quad to move it as this will only wear belt, Be patient it will dry fairly quicky. Remember to push plug back into belt housing.