Anytime you get seriously into the gooey stuff (Mud, people...I'm talking about mud here...although cleanliness IS next to Godliness with the other gooey stuff), it's time for some equally serious cleanup. Take some pics of the truck for later laughs. Then, get yourself to a powerwash and spend some quality time getting all the mud you can off the undercarriage, axles, wheelwells, wheels...everywhere. Expect to spend a lot of time (And if you don't have your own powerwasher, a lot of quarters) doing this; you want to be thorough. Then, like listed above, change ALL fluids. Oil and filter, transmission, transfer case (ATF will usually do) and differentials. Finally, after the powerwashing, the rig's gonna be screaming for grease. Hit all of the U joints, CV joints, steering parts, anything that moves and needs grease.
Then, when you're done with all of that work, think about how soon you want to go play in the slop again.
Been there, done that. Did you know that a replacement transmission for a 2001 Jeep Wrangler runs about $2300? I do. That's why I stay out of the muck as much as I can!