Son has a 1998 xj with 3-1/2" rubicon lift & stock 235 series tires. Not much 4 wheeling on long island, mainly mud puddles....where you shouldn't be anyway but managed to get it stuck in some mud & apparently spun the right rear tire on the rim. A soft tug by my STOCK '98 xj & it drove the rest of the way out. he drove it 1/4 mile out of woods, then about 2 miles home....tire low on air. drove 20mph & didn't notice any issues but 1/4 mile from home heard a pop, blew the tire completely off the rim. Since rim was already toast, drove it last 1/4 mile on rim. This morning put spare rim & tire on & now tranny doesn't shift-manually or automatically. If you rev it to nearly 4500 rpm's, it'll shift 2nd gear, didn't try for 3rd, but 2nd shifted several times.
Trashed tranny? Or anything external to look at?

 

You went mudding...how deep? Tps doesn't like water

 

pull the dipstick on the trans. make sure there is no water in there. some times when the transmission is very hot and is cooled very quick from dropping it in water, it can suck water from the pan gasket area and trash the trans. I have seen this happen before. it could have also sucked it in from the vent on the top of the trans housing.