Transmission Problem....Help Please!!!

Ok, did some wheeling today hit some deep mud pits and more water than i would have preferred. My buddy and i both had out xj's out playin in this stuff...on the way home..both of our alternators shot craps within minutes of each other...got mine fixed first then his...now i have a new little issue...the transmission is not wanting to shift through the gears...running about 3,000 rpms at 20 and wont go into any other gears....let the thing set and idle after hosing it off a bit under the hood...its shifting now but still erratic at times and doesnt seem to want to initally shift from first it hangs up i guess you would say...any one have this happen before??? Don't know for sure what i should look at TCU? TPS?? Now the orange check engine light is on as well...I'll get that checked out today but still any advice you have is appreciated...thanks

Check the TPS with a miltimeter....

What year is your Jeep?

The jeep is a 96 so it has the obd2 should be able to plug it in and find out the error code right??

stupid question where is the tps located is it mounted on the firewall just never looked for or replaced it before...

TPS = Throttle Position Sensor. It senses and reports the throttle position to the engine and transmission computers. It is located on the front drivers side of throttle body. They do not like getting wet (hate water) and malfunction once they get wet. Hard to dry them out too.

You should also check tranny fliud, if you lost power to your cooling fans when the alt went out you mught have overheated the fluid. If the fluid breaks down the trans may not want to shift properly.