A very common failure item are the input and/or output speed sensors. On the WJ vehicle, I'm pretty sure input and output are the same sensor (same part number).
At any rate, on this vehicle to check the sensors it's easier to remove them from the trans. The input sensor is closest to the front of the vehicle, and the output towards the rear. Both sensors are on the drivers side of the trans, and both should have a black 2-pin connector. Remove them and simply check the sensor for continuity. If the sensor reads open (no resistance), it's bad.
I once replaced an output speed sensor on a 45RFE, only to have the input speed sensor fail a month later, so now I encourage my customer's to just replace both--they can fail that often.
If you're in need of new sensors, you'll want to use OEM sensors, from the dealer. (I'm guessing 50-60 bucks each).
Not sure if this is the problem or not (am interested to know the exact PO codes stored) but figured we'd start you off with the most common things first.
Oh and no charge on the diagnostic time .... :-D :toothy10: