I am not a transmission man myself, but it sounds like the transmission is not engaging as it should, could be valves inside that aren't working right. A good transmission place could tell you what the problem could be. I think some valves work on pressure, and so it has to build up before the valve operates.
Although you only have 40000 on the rebuilt tranny, it could be giving you some problems.
Also, the condition of the engine, tune up wise, plays a big part on how a transmission works. There are vacuum lines that run to the tranny, on some vehicles, I don't know about the Jeep, but these lines work on vacuum, and if the engine is not running right, the vacuum could be messed up and so the transmission will suffer. Just another thought.