Sounds like the same problem I have with mine on my 89 YJ. I can set the mixture and idle on mine and the idle is dead on, then for no apparent reason, the idle will drop 300 RPM and the timing will drop 4 degrees. The neat thing is that it will still idle VERY smoothly after the drop, though I will notice what feels like a step in the timing and a power increase at about 1000 rpm.
Are you still running the stock ignition? I am, and I'm starting to think that the computer is screwing around with the timing. I'm about to replace the stock ignition with a Crane HI-6 that I have from a 280Z I restored a few years ago and see if that makes a difference.
Other than that, mine runs great too. Idles smoother than my buddies 4.0, so smooth that sometimes I have to check the tach to make sure it is running. More power, better MPG, no bogging.