Too easy- just clean and reoil the air filter, fire it up and get it hot, change the oil and filter.
If the oil comes out full of water, take it for a short run through all gears, make sure it's hot and change the oil again, but this will probably not be necessary.
The other thing to check is the ECU connector- under the seat, behind the tank, rubber boot with wiring going in- pull boot back, if there is any water inside, pull connector off, clean and dry out both sides- blow out with compressed air if possible- reassemble, making sure rubber boot is secure all round. Water in there can cause all sots of wierd issues in the future.
Don't stop in deep water again!