Ok I get all that use common sense but I have seen jeep video of water over the hood
If you keep moving (but keep it slow) the water level under the hood generally stays lower than the actual water depth surrounding the Jeep. I had my CJ with an open air filter in water over the hood more than once with no issues.
The way the grille is shaped on TJ's (and all Wranglers and CJ's for that matter) if you keep your speed around 5mph it will push the water down below most of the engine bay and avoid water getting in the air intake. The only thing you have to worry about is the radiator fan slinging water up into the air intake and as mentioned before you need to extend the breather tubes for the trans and t-case. The front and rear diffs are already pretty high (about the height of the top of the hood)
Not sure about how to extend the tranny breather on yours because I have a manual 2.5L. But as far as the diffs go the front tube is on the side of the radiator and the rear diff tube is on the filler neck hose. You'd need to just get some longer tubing of the same size and new clamps to secure them to the vent port on the diff. Then zip tie it up on the firewall or some thing.