Can you test the MAP sensor to make sure the thing is putting out the right range of voltages for the vacuum it is seeing?
We have a 2000 Cherokee with what is probably a similar setup (maybe not) and it intermittently runs REALLY rough. Usually it clears up within a few minutes or after shutting it off. no help i know.
I'll pull the vacuum line off of mine (drove it to work today) and see what happens just for comparison's sake.