misfire maybe?

Well, I've got a 1999 4.0L XJ. I just replaced the headers because they had a bad crack in them that they almost always get. After I put everything back together, the engine started up fine and ran fine, but once I started to drive it, it started acting really funny. So, when driving at low RPM's (about 1600 and below) it starts jolting back and forth. I keep the gas pedal constant and the RPM's go from below 1000 to where ever they originally were. If I leave it in idle, the RPM's start dropping and the whole engine starts shaking causing the entire jeep to shake. If I'm on the express way and in the higher RPM's, it never happens, but once I get on the city roads and into the low RPM's it starts back up. I'm thinking it could be misfiring, but the check engine light doesn't even come on. Any idea's what it could be?

Mine has been suffering similar (but not quite as bad) symptoms for 6 months. Idle semi-cuts-out about once every 2-3 seconds then comes straight back. 60+ cruising and WOT overtaking are fine. Cruising below 50 gives and occasional judder.

The spark seems good so I suspected the fuelling is the problem.

I have cleaned out the map sensor and throttle body with no improvement.

Gapping the plugs brought temporary improvement but it soon came back. Maybe an intermittently failing spark plug then - I haven't changed mine yet.

Well I replaced the plugs on mine about 20k miles ago, so they should be fine. Was thinking maybe it could be something with the injectors since i unpluged each of the electrical plugs when replacing the headers.

Make sure you didn't accidentally switch injector connection 1&2 or 5&6.

I made sure and labeled everything when I took it all apart, so they should all be correct. I'll still check though.

More then likely the heat soak issue. I wired my AUX fan thru a 5 post relay (so it keeps the stock wiring also) and another temperature switch so it comes on at 205 and goes off 195. I have not had any issues since with Hot start-up miss-fire.

Make sure your tps is plugged all the way in, make sure your map is plugged all the way in.

Unplug them, clean with electrical cleaner, let dry, use dilectric grease and make sure they plug in all the way.

I cant tell you how many times me and DrShaggford has forgotten to plug something back in or not all the way in.

Ain't that the truth....I would also check out the TPS as it can cause similar issues. If you pull the TPS and turn it and it sounds crunchy its definitely bad. There are also writeups on here as how to test it with a multi meter.