It doesn't matter who you are. Build your Jeep all you want and plan for every contingency, but the day will come when you drive your Jeep past its limits. If you are lucky, no damage will occur. If you are unlucky, you'll have some issues.
Rocks are rocks, and there isn't much that will kill a Jeep in them. Sure, a broken U-joint or axleshaft, some dents here and there, but really, the possibility of catastrophic failure is minimal.
Mud is a different animal. Get some water in your engine, and see how your Jeep likes it. At best, you'll lose compression in a cylinder or two. At worst, you'll hydrolock your engine, destroy your transmission and transfer case, and have some axle rebuilding to do. And that doesn't even begin to touch on sensors and electronics.
Don't get us wrong, mud is a great time, but the time will come where you drop your Jeep off an unseen ledge and a great time will end up costing three days of extraction or a new engine--or even worse.
What we are trying to say is this: If you drive mud, whether for recreation in the form of mud pit drags or because your trails all wind in and out of trees and streams, build your Jeep to handle water and dirt inside and out. Plan ahead, plan for the worst, and then plan for a foot or two of water over the worst.
Engine: Look, if you've got two months of the year where you don't hit any wet soil or puddles, waterproof your engine because you know you'll be driving in mud and water, so accept it. Put a snorkel on it and waterproof the distributor and the carburetor if you have one (even if you have to build a box around it to keep water out of all the orifices).
If you've increased the diameter of the exhaust, think about running a snorkel on that, too. Many engines will run just fine with the exhaust under 2 or 3 feet of water or mud, but if you are planning on 2 or 3 feet, you'll be seeing 4 or 5 feet in no time, so extend the exhaust. Think about it; planning on 3 feet of mud and water will cover your 35s. How many times have you or your friends lost 35s in the muck?
Make sure you've got an electric fan with an override to shut it off. An engine-driven mechanical fan can pull into the radiator, clutch or not. If it's really deep, loosen your belt(s) to the mechanical fan before crossing and retighten afterward.
Make sure all your electrical connections are waterproof; no twist and tape here. If you've got power steering, figure out how to vent that, too. Run the line to the same high point that all the other lines are run to (the stock cap doesn't seal well).
If you run really thick stuff, your radiator might get clogged and stop cooling. Experience is key here. This isn't really an issue if you trail ride, unless, of course, your trail winds around a wet field.
Transmission: Run the vent line to the highest point under the hood you can if your Jeep is a daily driver. If you've moved beyond that, run the vent line inside the cab to the top of the rollbar and/or tap the line into the top of the rollbar. Failing that, with all vent lines, use a stock-style plastic cap. The vent in some automatic transmissions is behind the torque converter with no provision for a vent line. If you want it to live, swap it out. Get something that has a vent line, or if you are handy, pull the transmission and block off the stock vent and drill and tap a real vent line in the case.
Transfer case: It's the same deal here as when it comes to the vent lines, with special attention needing to be paid to the shifter rails on earlier Jeeps. With deep submerging, the abrupt cooling can pull water past old, stock, rock-hard, shift-rail seals. After enough repetitions, you'll have a nice chocolate shake that will destroy your transfer case. Whether it's chaindriven or geardriven, check the 'case after every trip. Just pull the fill plug and stick your finger in. If water is there, you'll see foaming and/or bubbles.
Axles: Again, run the vent lines to the highest point possible; some people run them to the air intake, which isn't a good idea because there is a negative pressure in the axles and water can effectively get sucked in through the seals. The military uses a positive pressure on all drivetrain components when waterproofing, and it's actuated with a valve. While it's neat to see little air bubbles come out of all the drivetrain components, the system is very complex. Run your vent lines up high; tapping into the rollcage with a fitting is one way to go.
If you've got an open-knuckle front axle, find some aftermarket outer axletube seals or else your inner seals aren't going to be long for this world. Ditch the drum brakes.