Trailmystic,

The inlet for the filter is inside the fender between the plastic liner/steel fender.I doubt the engine actually ingetsed water,water and engines do not mix,not even a little.If you consider the size of the combustion chamber it takes very little fluid to lock the engine up.
More than likely the change in temperature of the engine,air(steam)and the chocking of air(initial wet filter) caused the engine to sense a rich/lean situation for which it over corrected and continued to do so til calmed down......similiar to the intake maniflod leak senario.
The engine senses extra air so it pours on the fuel,then it's to rich so it leans it out etc.etc.
I say you'd be ok,but a snorkel to control the splash into the box will be a good thing and if the front fender gets submerged before you can shut it off,a snorkle could save you from ingesting water,when the driverside falls into a trench left from like a 44bogger.

Bansil