I basically have the same setup other than the gears. I'm getting my auto rebuilt. I've replaced the filter about a year ago and flushed 1/2 of the fluid (can't do a real flush in my garage). Flushing a trans at home is very time consuming, fluid expensive, etc. You can only dilute the mixture. The trans needed rebuild as it was 'tired'. Shifts weren't quisp. THey were smooth. All gears went that way. Trans guy took it for a ride and said all this for when it was shifting. He manually shifted and showed the difference for being in the proper rpm range and how the trans shifts. Any type of hill I ran into, foot was to the floor. If the trans didn't down shift, I would do it manually. THis shows the trans is slipping and heating itself. I do have an extra cooler on it. Trans guy says that is not necessary for the way I use my TJ. Heat does hurt the auto, but I'm not generating any trans heat per se. Putting the trans into a load, constant or some time, creates heat. Crawling on the trails, driving on the street, etc doesn't create heat that the original cooling can't handle. There is a 'ball valve' on the cooling lines (feeder to the cooler) where Dodge added a plastic ball to minimize the amount of drain the trans gets just parked.
Rebuilt trans, flushed cooling system and I'll be good to go. I'm doing the swap myself as my skid probably won't go back up once taken off. So I'm building a flat skid and doubling the tcase. I'm expecting to do this in about a month.
Get the trans checked out by couple auto trans people. See if you can find someone that you trust to rebuild rather than a shop. A more personal experince I prefer for those with knowledge rather than a shop convincing you what you need.