Does it sound like you have one cylinder that is not firing? A lot of times a rough idle will be caused by one cylinder that does not fire until you hit a certain RPM say 1200. Every time that piston comes around when the next one in line fires it hits pretty hard because the bad one didn't fire and allowed the engine speed to drop.
It looks like you have already started on the 2 most common causes if that is it, the one I have seen the most is the gap on one of the plugs is to wide. At low rpm there is not quite enough power to jump the gap, but once the rpm's speed up you get enough power to make the jump and it starts firing. You can re-gap them all or figure out which one is doing it and just re-gap that one.
The other one you have already started is if one of your injectors can be slightly clogged, at idle not enough fuel is getting through, but when you increase the pressure you get some fuel through(though still not as much as you should). You could clean/replace the bad injector.
If it is the cylinder thing it is pretty easy to figure out, just pull a plug wire off a plug enough for it to not spark and start the jeep, if it sounds even worse or wont run at all then you will know that it isn't that one. One of them will make the jeep idle exactly the same weather it is hooked up or not, that is your culprit.