First thing is to make sure all your seals are good. Make sure your hubs have a good o-ring on them to help prevent a lot of water from getting in them.
Next is more of a chore. Breathers. Stick a piece of 5/16" hose on your differential and route it up higher. Usually I put mine on top of the fenderwell (between the outside skin and inside skin of the box) but I've been zip-tying mine to my filler neck on my truck. Make sure you keep that mushroom end on the hose. I figure if I'm that deep I'm going to have water in the fuel anyway.
Route the front axle's breather to the core support and take it up as high as you can while keeping it recessed under the edge of the core support.
The transmission breather is really small on the top of the transmission on the driver's side half. It points backwards. It breaks real easy so be careful. I either used 5/32" or 7/32" vacuum line on mine. I routed it up to firewall by the vacuum canister on the driver's side.
The transfer case has a little piece of hose (3" long perhaps?) hooked to yet another one of those mushroom things pointed forward. 5/16" hose will work here too. I ran this up by the vacuum canister.
I don't like to go in water because I have bad tie rod end boots and such but it can be fun. Oh yeah, and if you've got a bad floor mat or a hole in your floor you're going to rot out your floor. I gave up and don't have a floor no more.
I learned about waterproofing after I drove through some water that made my fenderwells disappear. I was alright until I got hung up on a rock and log in more shallow water and then I started taking on water. It took the Explorer two trucks ahead of me an hour to get running again.
Mud lines are cool... just not on the inside of your doors.
I took a picture of the horsehair mat wet. I threw most of that away. I put the vinyl floor back in. After the next time I took on water I never put the vinyl back in. It kind of sucks when you go wheelin' with guys that consider 33s to be "little" tires.