If u went deep enough to get your air filter wet I GUARANTEE you have water in both diffs/t-case/tranny. Even with all breather tubes extended it's possible to suck air/water straight threw your RTV seal on diffs if they were really hot and you plunged into cold water.

Start with the t-case and when you see white/milky stuff come out change everything else. Ask me how I know..... Sometimes I think my TJ is a submarine )