well check everything. axles, hubs diffs, sounds like you got a flooded truck.
the only way that I can think of to get all the water out, would be to either change oil alot.. or open everything up and let it dry.. maybe a hellll of a bunch of wd40??? or alcohol fill it and let it sit for a few hours and drain it all back out. would be helll on the seals.
or open, drain, blow dryer or heat gun.

thinking about it over again, I think that I would go for the drain, pull all the drain and fill plugs shifters and use the heat gun.
or a garden sprayer with the alchol and wash every thing down really good, then the heat gun AFTER the alchol is gone.
good luck, I would like to hear how this turns out.