While I don't think your issue is the TCM, technically it should be compatible as the Prowler uses a slightly modified version of the 42LE. I would not, however, look in that direction. When changing a TCM (or a transaxle) you should have a dealer clear the CVI table (clutch volume index, it lets the computer keep track of how much fluid is required to actuate the clutch packs). Out of whack CVI values will throw a wrench into things and while I think the TCM can learn new values over time, that's not a given and correct procedure dictates having the CVI values cleared.
Now, on to your problem. I would look at fluid, filter and o-ring. The transaxles in these vehicles are particularly sensitive to fluids so ensure that you always use ATF+4. I even tend to only buy the Mopar branded stuff, there are other brands, but I think it's best to go with the genuine product. I would replace the filter and o-ring and clean out the pan sump and replace the fluid.
I would do that, and ensure that your fluid level is correct first before continuing any diagnostic. Some might say that you should just check your level, and while I would tend to agree, there is a strong likelihood that your transaxle is filled with ATF+3 and ATF+4 has a more up-to-date fomulation so it is a good upgrade regardless. If other people have serviced your vehicle it is possible that they used the wrong fluid altogether, like Dexron, and if thats the case, you want all that shit out of there ASAP. In fact, I don't know if there would be any salvaging that transaxle short of a complete rebuild if that is the case, but if you have a chance at all, it starts with removing all of the contaminated fluid - and in the even of improper fluid fill, I know of very few ways of ensuring you are able to completely change the fluid out aside from diluting it with several changes, and that could get expensive. Some have recommended Jiffy Lube type flushing, and in the even that you KNOW the fluid has been contaminated with a non ATF+3/4 product, then I would say it probably couldn't hurt, but otherwise, I would recommend staying away from that procedure, others may disagree though.