First off, you did the first thing right, by not going in till you were prepared.
You should definitely vent your front and rear diffs. Before I vented mine, a diff oil change after a trail ride would look like a milkshake mixture <img src="/forums/images/graemlins/shocked.gif" alt="" />. If you have an auto, you can find the vent on the top of the tranmission. I ran mine up to the top of the firewall, and terminated with a fuel filter. Ditto on the transfer case.
As far as the air intake, a snorkel is obviously the best idea. Airtech and Safari are two brands available.
In terms of water entering, there's not a lot you can do about it. The Monty door seals are pretty good, but if you go in far enough, you will get water across the floorboards. Have a look around your interior and get a good idea of where your electronics sit, and don't go any higher than they sit. GenI computers are behind the glovebox. Locate yours and don't get it wet. I pulled out the metal drain plugs and replaced them with rubber ones, on the offchance that I did get water in. Made it easier to get it out.
Driving style has a lot to do with how successful you are in watery situations. A steady pace to create a bow wave after slowly nosing in is usually the best approach. If you stall out halfway across, don't attempt to restart. Get towed to the other side and then take action.
I always carry a can of WD40 with me, and spray the dizzy cap before entering the water. I also hook up my tow strap beforehand, and bring it back over the hood and set it in my lap in case I need a quick extraction. Also a good idea to carry a spark plug wrench in case you need to pull the plugs after water ingestion (hydrolock bad).
When you get home, be prepared to do more maintenance. Difficult to keep water out of hubs/bearings (if you got em), and its good to check for water contamination everywhere else.
Oh, but have FUN! <img src="/forums/images/graemlins/smile.gif" alt="" />
PHIL