If its a 3.6 auto, the trans/and transfer case breathers are high up behind/on the engine so its unlikely they were submerged.
I extended my front and rear diff breathers cheaply and easily using a couple of 3/8" tube joiners, some 3/8" fuel hose and a pair of cheap 3/8" fuel filters....the front one is up near the fusebox under the hood, the rear one up behind the RH tail light inside the quarter.
If you need to do deep crossings, get a poly tarp and cover the nose and bullbar....it forms a nice air bubble in the engine bay during the crossing.
Personally, I'd drain your diffs .... to be sure.
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