Plan on replacing any roller , needle and ball bearings as well as their races, the water will have rusted and scored them if it has sat that way for any amount of time. You'll need to take a close look at all the gears as well. This means a complete tear down. Is the truck it is out of a 4x4? Trucks that have done a lot of river crossings commonly have this problem. I bought a truck many years ago now that had a transfer case in the same condition as your transmission.......the PO loved to cross streams with it!
-Mike-
