I am having the same issue with my 2000 Gr Cherokee 4.0. It will start up and run perfectly, once it warms up a little and sometimes it happens once it warms up all the way, but it happens everytime I drive it. It bucks and backfires, and misses. It then stops all together after giving it some gas, and then its fine the rest of the time until it gets cold again and I start it and drive it again.
Im just starting to diagnose, was wondering if you came up with anything, or if anyone knows where to start. I'm thinking intake leak. Faulty fuel pump. Faulty fuel relay.
It has new plugs, new air filter, it has 177,000 miles on it. It's definatley weird, that it only does it once it's warm, and only once at idle , but then at idle for the rest of the time it's running, no issue.