well, you said you were hitting water, there could be the chance of it splashing into the air intake, enough to do engine damage but also sucking in wind, it would push all the water through showing none so it may not seem to you that theres water in the intake.
Also, its possible for a seal to not be "sealed" basically and water leaked through while hitting the water.
But none the less, drain it, which I'm sure you've done, pull the plugs and try and pull start it to push the water out of the top end of the cylinders. Then once you finally do it get started, let it idle enough to warm the engine up, getting the oil sloshed around, drain the oil again, repeat this until the oils no longer milky, then just take it easy on a small ride not very far, check the oil, if its milky, change it until thats gone.
Do not try starting it with water in the engine again.
But you said it was bogging in the top end, when I sunk my bike, same thing happened, get all the water out and all that, take it into the dealer, don't say there was water damage because they will charge you and you still have warranty, get them to do the valves because you no longer have compression because of the water bending the valves. This is VERY costly I've had to do 3 valve jobs since I sunk mine.
When you get it back sell it, it will never be the same unless you buy entirely new valves for it, its been ran with water in the engine so its gonna need a rebuild soon because that messes up your motor badly.
But none the less good luck with fixing it, if its hard to start when you get all the water out of the engine, thats your valves gone and you have no compression, so once its ready to be started and its hard to start, go on the side to pull start it, and hold the throttle open about a quarter, choke on full and pull it out until it hits once thats your compression, pull it past that hump, then pull it really hard to fire the engine. This will take several tries.
