Water in Engine
 

What is the best way to clean the engine once it is dropped in the creek? I was reaching for the kill switch when it died so it was running when it went down. Can it be cleaned without splitting the case and by just removing the cylinder? I did not start it once we got it out of the creek.

do it soon !
 

Hi,
I know that you need to get the water out asap before it damages the main bearings( it may be too late.)
There is a drain plug (allen) for the crankcase on the bottom of the engine ahead of the trans drain. Remove it. Remove the air filter as it also probably is flooded. Remove the spark plug. You can spray some wd40 into the intake tract and then kick the engine over repeatedly while holding the kill button. Clean the plug(dry the plug) put it in and try to start the bike. If it starts, don't rev it more than you have to until it warms up. Once it is warm, it will have dried itself out (crankcase, cyl, etc) but you will need to drain and refill the trans. Remember the air filter is off so get the loose dirt out of the airbox 1st.
Another way is to attach a shop-vac(wet/dry vac) to the exhaust flange(remove the pipe) clean the flange and use duct tape, or hose clamps and anything you can use to make a junction between the vac hose and the flange(maybe a rolled up piece of cardboard or a cut up milk jug) Then get a blow drier and blast it into the airbox(filter removed) while holding the throttle open. You might want to pull the slide and cover the top of the carb so max air can flow. Now you have to turn the engine so the piston clears the port at the reeds. blow the hot air in. When the cyl feels warm from the blow drier you can then put the engine at tdc turn on the shop vac.

part 2
 

with the shop vac on you are just trying to get any moist air in there out so move the piston up and down a bit to expose new areas to the suction. Then hopefully you can put it together and start it.
Oh, Make sure you drain the carb bowl, and put the drain plug back too (before you try to start it)When it starts, shut it off, put on the pipe, restart it and warm it up.
Good luck!

Make sure you drain the water out of the pipe. You shoud repack your silencer too.

You can flush the motor with kerosene too.

Cleaning water and sand from engine
 

This was just my second ride on a new top-end so I wanted to keep the damage to a minimum. We drained the exhaust when we took it out of the creek and then towed it in. I removed the carb and reeds then flushed it out with diesel from a pump up sprayer. I rotated the engine slowly while spraying the diesel in the crankcase with the crankcase plug removed. I then removed the cylinder and it was loaded with course sand. I covered the crankcase opening with a rag then cleaned the piston and rings with carb cleaner. I then sprayed more diesel in the crankcase and especially in the ports that lube the crankshaft. I rotated the engine while I sprayed. I then poured premix through the crankase to clean out the diesel and lubricate the crankshaft. I think it is pretty clean now. I rode it once since then and it seems to be OK. I guess only time will tell.