Ok, everybody is concentrating on the worst case. That is fair. What about the best case scenario? That the water was high enough to wet the air filter but not high enough to flood the intake, leaving the engine dry? That there was water only in two cylinders, the rest are totally fine? That there is no trace of water in the tranny or the axles? All possible.
I know I would have a case of beer ready when I did the first preliminary inspection, draining the diffs, the tranny , the oil sump and see what's what.
All the best for your project, these trucks are tough as nails and I hope she ain't as bad as in theory she could be!