What kind of battery are you using. Does it have enough amps to run all the lights on the Jeep for extended periods of time? I find it strange that this situation would have anything to do with a drained battery as once the engine is started the power that the vehicle uses comes from the alternator/voltage regulator system. Have you had those checked out?
My vehicle died recently up in the mountains ($150.00 tow). It turned out to be the cam position sensor (located inside the distributor) and the coil. The sensor was about $40 and the coil $25.
1993 ZJ Limited 5.2 - no mods - Red with Gold (what were they thinking) trim.