Ever replace your motor mounts?
If not, take a look at them. It it looks cracked, or dry at all, then they probably need replacing.
I tried everything to get the idle to not be rough (idle was worse in gear, which explains the bad mounts). I finally caved and had a diagnostic done. Everything checked out. They said the engine ran great, but I'm gonna want to replace my motor mounts soon (and while I'm at it I might as well change the tranny mount). They said I pretty much replaced and did everything that could have to diagnose a rough Idle, and preventative maintenance. Compression tests, vacuum test, new spark plugs, wires, distributor cap, rotor, o2 sensor, idle air control, air filter, fuel filter, cleaned throttle body, vacuum lines, ccv orifice, new tranny fluid and filter, thermostat, for the idle, and many other parts that just went out (probably from the engine's violent shaking at idle) like the water pump, and starter. I'd also replaced other misc parts like the serpentine belt, shocks, and differential flush and change, and recent oil and filter change, and lubed the chassis.
I just got done putting on the mounts today. Holy crap. It literally feels like a new vehicle. engine is nice and quiet, no vibrations at all come from the vehicle, and when I shift it in gear, omg. Heaven.
When you start it, does it shake the vehicle a bit whenever the engine cranks to life? when it's in gear, does the rough idle get worse? It's probably the mounts. They told me that the 4.0 is a very unbalanced engine, and when the mounts go bad, every little part of the unbalancedness gets transferred to the body. It can seem as though it's misfiring intermittently, even though vacuum tests and compression tests say otherwise. After I replaced the mounts the "phantom misfire" was gone, no rough idle, no shakes, no vibes.
If not, what have you done to try and diagnose the problem? Is there oil on your air filter? if so, your CCV orifice is clogged, and needs cleaned or replaced. That can cause a rough idle. You've already replaced the IAC, so it can't be that. You could have bad compression from worn piston rings, but you could have other problems with that. fuel filter could be clogged, o2 could be wigging out, sometimes platinum plugs in the 4.0 can cause some problems and you could switch to new coppers to try that. New ignition coil, wireset, distributor cap, and rotor can fix a lot of problems. Check your engine for codes. All an engine needs is Air, spark, and fuel to run, and to run right, it needs good spark, and the correct fuel and air mixture at the right timing. So try and eliminate it down to one and go from there. if you've replaced the dist cap, rotor, coil, wires, and plugs, and that all checks out, you can worry about whether it's fuel or air related.
The best way for diagnosing this kind of stuff if a compression test and vacuum test. they show a lot about what the engine is doing.