UPDATE:

After running great for 2 days, the rough idle/misfire has returned

CEL returned -- Misfire Cyl 1 again...

What. The. Hell.

Is this a Distributor issue? I pulled the cap and it looks fine. Rotor as well.

Help...

I realized it has been disagreed with, but try the 91 octane. The issue is the ethanol in the gas that doesn't allow the gas to atomize as well as it should. When we go to smog in CA, we always put in the high test. A marginal carbon emission will pass that way and save getting a new cat

Did you ever change the spark plug to cylinder 1 ? , The spark plug could be the real problem .

I replaced plugs, wires, cap and rotor. Did the wires/plugs first with no improvement. Then replaced the cap/rotor (see pics previous page), and the misfire/idle issue went away...

Today it returned along with the CEL and a P0301 code (as it did when the original problem began).

After doing some more research, and because the new cap/rotor SEEMED to fix it for a short time, could it be the COIL??

I was reading though every thing and it looks like you never changed the coil , a weak coil can be the problem and looking at all the things you changed its a cheap part .

NOT the Ignition Coil...replaced.

NOT the fuel pump/fuel pressure... 45 at KOEO, and 49 at idle...

Is the Leak Down Test the next thing!??

That's where I'd go next, and/or pull off the valve cover and inspect the valve springs and rocker arms.

Have you tried the steam cleaning? Sounds crazy, but sometimes it works.

What am I looking for by pulling the valve cover? Would there be something that I would see with the naked eye that would explain the rough idle/misfire? I'm not hearing anything that makes me think that there's something amiss there aside from an occasional "tic-tic-tic.." sound which I BELIEVE is fairly normal for the 4.0...??

As far as "cleaning" goes, does Sea Foam do the same thing that "Steam Cleaning" would do? What are the benefits of doing this?

Seafoam treatment done... NOT a lot of smoke (like I've seen in some videos), which makes me happy that the internals are fairly clean.

Followed the guides (into gas tank and brake booster hose--no crankcase, yet), took it for a 20 mile roundtrip--running it hard when possible--and I'll be damned if the chuggy-feeling, rough low idle, and response didn't improve dramatically by the time I returned home!

Time will tell, and after the last "fix" I thought I had, I'll wait a bit before confirming success, but there's no doubt the Seafoam made a difference.

My question is, was this most likely a scenario where I had gunk on a valve that was preventing it from operating at 100%?? Something else that makes sense??

Weeeellllll...

Give it a few days to make sure it actually fixed it. It's not uncommon for one of us to try something that makes it behave as if it's fixed, only to have it crap the bed again a few days later.

Do you normally take short trips, drive it pretty easy and never get it above 3200 RPM? If so, the cause of all this may be the valve rotation issue noted in this TSB:

http://www.wjjeeps.com/tsb/tsb_wj_0900303.pdf

So it could be that the #1 exhaust valve is not rotating properly. I think I would try to drive it for now and see if it starts misfiring again. If it does, I would pull the valve cover and look to see if the #1 exhaust valve stem has a bullseye or a line on it as described in the TSB. If it does, do the procedure in that TSB.

Good luck, and let us know how it goes.

Even though this is an old thread I wanted to add some knowledge in case it helps somebody else. I just went through a similar situation. Rough idle and p0300, p0301 codes. Other than that seemed to run fine. I replaced the plugs, wires, cap rotor, coil, distributor pickup, tested injectors, tested fuel pressure, tested compression and nothing was solving it. Talked to a friend that owns a mechanic shop and he said burnt exhaust valve is common on the 4.0 and to do a running compression test and I'll probably see an about a 15 psi difference on the cylinder with the misfire code. I'd not heard of a running compression test before but it's the same as static test except you start the engine and let it run. When the engine is running use the release on the pressure gauge and let it build pressure while you watch it because the initial cranking to start can give you a false reading. I did this and my number one cylinder was 65psi and the others were 80psi. I then took my head to a machine shop and sure enough number one exhaust valve was toast and the other exhaust valves were far enough gone they need to be replaced as well. Ended up having all new exhaust valves and hardened seats installed and the engine runs like normal again and no cel.