What it is: '99 Cherokee, 4L I6, 106k miles

What happened:
Water pump seal went out, coolant got too low, blew lower hose on freeway, water temp went to max just as I was exiting. Coasted in to store parking lot, removed hose, taped it up, added water, limped it home. Got a CEL, misfire on #1 cyl.

What I did:
Removed fairly new radiator and flushed, back flushed heater core, installed new water pump, hoses, thermostat, filled coolant and purged air. New spark plugs. Cleared CEL

What's Happening now:
Starts fine, idle is very noticeably rough. Seems to run fine except at very slow speeds it's rough. I have run it about 25 miles up and down a steep canyon. CEL reappeared misfire on #1. I have looked at the #1 plug a couple of times, it's a bit prematurely dirty but does still fire. Cranked engine without plug and got a tiny bit of water mist out the plug hole, nothing alarming. It seems to be mostly running on all 6 cyl and somewhat intermittently on #1. From a cold start, #1 header heats up fine but the idle is still rough. If I pull the #1 injector wire it gets much rougher. I still get a CEL and have cleared it severl times. I don't seem to have a vacuum leak. No steam coming out exhaust. No apparent power loss pulling steep grades.

I pulled #1 plug first thing in the morning and cranked the motor, no water came out, put plug back in, started and idles rough. I suspect I have a very minor coolant leak thru the head gasket that is causing the rough idle and CEL along with intermittent misfire.

Any thoughts? I really don't want to pull the head If I don't have to, but I'd like to cure the rough idle. Any ideas to confirm coolant entering the combustion chamber is causing the misfire? Any other diagnostic tricks?

TIA, Nick

find someone with a combustion gas tester. you put it in the radiator to test for the presence of exhaust gas. this would be the easiest. Also you could find a leak down tester and try that also. Maybe try a compression test but I dont think it will show up there.
Either leak down or gas analyzer.
To add, how is the temperature while it is driving? is it pushing out any coolant, or using any?

Checked this morning, it's using about 2 quarts in 50 miles. When getting a bit low the temp creeps up.

I think pulling the head's in my near future.

start the engine cold and hold rad hose a leak in the head gasket will be worse cold due to expansion! while holding hose crack the throttle a couple times and see if the hose swells up or builds pressure really fast if so combustion is entering the cooling system! that would also explain the rough idle but ok crusing

also just a tip when doin the head if neccessary be sure to insp the gasket very closely if no obvious sign of a leak it would be in your best interest to send the head to a machine shop and have it checked for cracks 4.0 heads have a tendency to crack around valve seats sayin this based on experience work im a tech in a jeep dealer and deal with this stuff daily just a tip

Performing a compression test on all cylinders is the best and easiest way to snake out a potential head gasket issue.

The spec for the 4.0 is 120-150, with no more than a 30 psi variation between cylinders.

An hours worth of work and you will have very valuable data. Parts stores will rent you a high quality compression gauge if you don't have one or have access to to one.