Hi Jim, I drowned my bike yesterday further along this innocuous looking trail.
Riding through a puddle and the bike dropped away, up to the airbox in water. I hit the engine stop quick and pushed it out. Spark plug out, fuel off and plenty of kicking over with the throttle open. After that, it fired up no problem and ran fine for the rest of the day, so I think everything was ok.
I don't think there's that much you can do to prepare the Gas Gas airbox for water because it is so open. Being prepared to stop the engine quick if it's going to take on water is the main thing. Before crossing a river, I always stop for a moment a remind myself where the stop switch is because the bike will go over fast if I hit an unseen rock at the wrong angle.
On the same subject, if the bike coughs and splutters when crossing water that isn't so deep as to get in the airbox, most likely water is getting into the flywheel housing and disrupting the generator. This can happen because the plastic cover is fitted badly, or water is getting into the housing through the mysterious hole in the engine case which has a pathway to the flywheel (indicated by nails):
The solution to this is to plug the hole with an M6 bolt. But if you do this, it is important to remove the flywheel cover after cleaning the bike and allow the condensation created by air temp differences to escape. In the picture, the crankcase drain bolt can just about be seen. This is the large allen headed bolt on the underside of the cases, and is the one to use, instead of the spark plug, if the bike has taken on a lot of water.