I must of missed the part about the snorkle being connected.
From the pics, it appears the airbox is still connected. I also see a flex hose behind it going somewhere.
Extend the breathers in front and rear diffs and the transfer case.
How did water went into transmission? I see the fill port is above the water in that pic.
There is a tiny drain hole at the bottom of the air fliter box. If you leave it 3 hours, there should be plenty of water in the air box.
So dajavu ...
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get ready to pay for a trans too. its extremely hard to get all the water out of them.