Is the vent something that only automatic transmissions have? In my first jeep (manual transmission), armed solely with ignorance, I ran through lots of water and ended up drowning the engine even, but had no issues with the transmission.
I also have a 98 tj sport auto. 4" lift on 33's. Usually have no problems running through about 3ft of water, then about two weeks ago I stuck in about two. Just got caked up. Definitely don't want to let her shit there for long. She was down for about 5 minutes til the wench was set. But once I got off the trail it wouldn't come out of first for about 1.5 miles. Then was in second for about two day before I went and had it flushed with new filter and gasket. And after still took about another day before she ran right for me. Been stickin to the rocks lately. Thought I was invincible with front and rear lockers. Not in the water.