the pistons and old valves had some carbon on them, but not so much that I would think it caused any issues.  I have little experience here, and it's a 139k motor, so what a isaw looked reasonable to me.

I did pull the fuel rail when replacing the head, but did nothing more than looking at the face of the injectors and dumping some of the gas out of the rail.  I frankly didn't know how much I could mess with them before doing damage.

One other thing, regarding the high idle, as I roll to a stop, the idle is initially quite high, at about 1500rpm, and it seems like it takes a second for it to 'recognize' that it's stopped and should reduce the idle speed.  After 4-5 seconds, it seems to register, and drops the idle to a still high level of about 1000-1100rpm.  I read awhile back that the spedo sensor can cause issues like this, and I'm wondering if it may also cause misfires to be registering too.  I think the post mentioned both, but again that was a few months ago.

It's still in the back of my mind that I'm missing a vac leak somewhere, but if so, I haven't been able to locate it.  

check gasget under throttle body and bolt may be loose  

High idle usually relates to an intake leak.  I am also thinking in this day and age of electronics that the manifold pressure sensor may be off.  The computer uses this reading to adjust the a/f ratio.  If this is off, then you may be too rich/lean causing misfires randomly.

With most vacuum sensors that I wave worked with, you can use rubbing alcohol to clean it.  An oil film can make the sensor give a faulty reading.

Hope any of this helps!!!  

I loosened and then retightened the manifold bolts and got the idle back to normal.  However, while it ran better for a bit, the CEL came back on with the misfire codes.

It seems that I can clear the codes and then it runs fine for at least one trip, but if I shut if off for a while (long enough to cool down usually) the CEL and misfire codes come back once I start driving again.

I have not done much checking on the fuel delivery.  I do know it primes fine when the ignition is turned on, and seems to hold pressure pretty well.  (I listen for the fuel pump when turning the ignition to 'on' and it only runs for a very short prime time if I try again within a few minutes)  

Also replaced the MAP sensor.  Which obviously did not help the problem.  

I have issues with my tj that sound a lot like yours. 99 TJ Sahara 4.0... it all started around 2 months ago, driving down the road at 50 MPH and then all of a sudden the engine cut out completely, as i am hitting my turn signal and heading to the sidelines it starts up again and runs like nothin happened. The problem got worse, sometimes the jeep would run for a week and then do it again. After replacing a few thing... TPS, crankshaft position sensor, oxygen sensor, distributor, coil, plugs, wires, and cleaning the intake air pressure valve, and removing the injectors and cleaning them... still same problem but now the jeep runs just fine on a hot day but in the cold morning it runs like crap !!! What the hell could cauze the damn jeep to run like *** only when the weather is cold??? Well after hours of working on the jeep looking for the issue i found something... the oil pressure guage was higher than normal on pressure and the jeep ran like crap, when the guage dropped down to normal pressure (after the engine was warmed up completely) the engine ran fine. If the weather was cold the oil pressure would be high. The oil pressure sending unit send the oil pressure info to the computer, when the oil pressure is out of normal range the computer turns off the fuel pump. I have a new oil pump in my hands and i will do a engine flush before dropping the pan and replacing the oil pump. Anyone have any sujjestions for flushing the engine???  

I'm no help on the engine flush, but all of my searching has led to the fact that all of these types of things can be related.  If possible, you may want to see if the intake temp sensor is reading right.  I also saw in my searching that there was a TSB out for cold weather misfire problems that includes possible 'cures' of software updates and top-engine cleaning.  

UPDATE OCT 1 08:

The Jeep spent 2 weeks at a local Jeep-only dealer as they tried to figure out the misfire problem.  They checked and adjusted some of the electrical systems and made sure the timing, fuel pressure, compression etc are all in spec, which they were.  They feel that it's a mechanical problem, which they say is bad cam/lifters.  They feel that there is a gradual leak-down at the ifters which eventually leads to the multiple cylinder misfires I'm getting.  They also say I need to replace the cat soon because of the amount of fuel that's been getting dumped into it.  I have a brand new one handy so that's not a problem.

I asked if there was a likelihood of doing further damage driving it with the random misfires going on, and they didn't think it was an issue.  I'm still not convinced that this is the issue.  When I replaced the head, I pulled the lifters and the bottom of them was smooth and not worn away, and the lobes of the cam I could see were also free of visible damage.  I'm not eager to pull the engine engine apart again, especailly not with the additional fun of pulling the grill etc. to swap the cam.

I'd welcome further thoughts on this!  

I have a 96 xj 4.0(175000m) with the same exact symptoms. The ruff idle, Misfire code, ect. It makes good power when you get on it and the engine shifts down. When you let it go back to 4th and maintain about 50mph at 1200 rpm, there is the misfire and you can certainly feel it. The hot cam description for the idle is perfect. Here is what i have changed and tested. I bought the car used and had the problem show up after an hour ride home. Though the idle is a little ruff. It is consistant, normal RPM, and dosent hesitate or die when you start or stop.

1.cps- I figured what the heck and i now have a spare for the trail
2. Used Distributor, mine had alot of lateral play. Rotor was scraping the cap terminal. I used the cam sensor from the replacement Dist. I also had the timeing off one tooth the first time i did this. Got it straight now.
3.plugs, cables, cap, rotor
4.Rear O2, original was broke off
5.Replaced CAT with test pipe. put a spacer on the O2 so dosent get too hot, also relpaced muffler with a cheap turbo muffler.
6.Did the Top end Decarbon thing with sea foam. 3 times
7.TPS replaced
8. Trottle body removed and cleaned
9. Idle air valve removed and cleaned
10. changed a couple of vac fittings and check valves that looked suspicious. Cant find any leaks though.
11. Leak down compression check. all were 5 to 10 percent loss except the #2, which was 35 to 40%( the low end of what i think is acceptable.) I also had the Valve cover off and could tap on the valves. didnt get any better valve seating. also turned them, didnt help increase compression
12. Fuel pressure test at the rail. about 50psi so it was ok. Put in a fuel filter.

I guess my next thing is to check the Coil. I am also going to check the plugs for the injectors. The metal retaining clips are gone and the plugs unhook very easily. I have a set of 5.0 injectors i want to install. Im not sure if they are the correct gph rating or not, need to check still. I also have the bigger intake from a 2000 i want to put on at the same time. The misfire problem was not there today after an hour drive. But after 30 more mins of several small trips it was back. I only thing i did differently before it improved was that it was left at the airprot for 12 days straight. I only get to work on this thing once a week. When I make my changes i will update. My friend has a 96 also and has been helping me with this.
He has a descent OBD2 code reader with the Freeze frame and live data recording. I am learning how to use it each time and we havent seen anything realy strange yet. Since my misfire seems to be comeing and going now. i dont think its a mechanical issue. (Bad Head or Dist.) We are thinking electrical. I will change or repair the head after everything else is checked. It cant hurt, Right. It sounds like we have the same problem. Again ill check in if after the changes. Buy the way. I too, have been driving mine the way it is.  

I know this has been discussed but I am having the same issue with my 2.5 4 cylinder.  I really appreciate the tips!  Here is a TSP from CHrysler I found
Tech Tip: Jeep Multiple Cylinder Misfire

In September 13, 2007 / default

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Models affected (applies to vehicles equipped with a 4.0L engine):
1999-2001 (XJ) Cherokee;
1999-2004 (WJ) Grand Cherokee (All Markets);
1999-2004 (TJ) Wrangler; and
2001-’04 (WG) Grand Cherokee (International Markets).

The customer may experience an incident of engine misfire during certain vehicle operating conditions. The misfire may occur when the vehicle is operated between 50-70 mph and under light loading conditions, e.g. slight uphill road grades. This condition may occur at all ambient conditions, but is more noticeable when ambient conditions are less than 0° C (32° ***

If the vehicle is OBD equipped, an MIL illumination may also have occurred due to DTC P0300 - Multiple Cylinder Misfire. Various single cylinder misfire DTCs may also be present. If the frequency of misfire is high, the PCM may place the engine in “limp-in” mode.

The misfire condition may be caused by one or more engine exhaust valves that are slow to close. Late closure of an exhaust valve may be the result of no valve rotation and associated buildup of carbon on the exhaust valve stem.

DIAGNOSIS

1. This condition may occur when the engine is not allowed to run at engine rpm that are greater than 3,200 rpm. At 3,200 rpm or higher the engine exhaust valves will rotate if not impeded by high carbon deposits. Low engine rpm and high carbon deposits are associated with short-trip driving where the vehicle engine is not allowed to fully warm to normal engine operating temperatures. Cold ambient temperatures will increase engine warm-up time and add to the opportunity of carbon deposit buildup on the stem of the engine exhaust valve.

2. Verify that an engine misfire condition is present. Use of the DRBIII during a road test, or a Co-Pilot data recording, may help to determine engine misfire and misfire counts. If carbon deposit accumulation is severe, then a cylinder leak down test may detect one or more cylinders leaking greater than 15%. Save any misfire DTC freeze-frame data that was stored for later misfire correction verification.

3. Verify that the engine misfire condition is not caused by faulty engine mechanical or electrical components.

4. If the engine mechanical and electrical systems are operating properly, perform the Repair Procedure.

REPAIR PROCEDURE

Inspection:

1. Raise the vehicle’s hood.

2. Remove the engine valve cover and all six exhaust valve rocker arms (the intake rocker arms are also removed during this step). Refer to the appropriate vehicle service manual for detailed removal instructions. The valve cover gasket is reuseable. Keep each pair of rocker arms matched to their respective valve and cylinder.

3. Inspect the end, or tip, of each exhaust valve stem where it makes contact with the respective rocker arm.

4. Determine if each exhaust valve is rotating within its respective valve guide. An exhaust valve that is rotating will have a “bulls eye” or circular wear pattern on the face of the valve stem tip. If the exhaust valve is not rotating, a straight mark-like pattern will be present across the face of the valve stem tip.

5. If there are exhaust valves that are not rotating, then proceed to the Valve Rotation section of this Repair Procedure.

6. If all exhaust valves are rotating, then this bulletin does not apply and further diagnosis is required. Install the engine rocker arms and valve cover. Refer to the appropriate vehicle service manual for detailed installation instructions.

Valve Rotation:

1. If one or more engine exhaust valves are not rotating, perform the valve rotation procedure to all six exhaust valves.

Note: It’s important that the Valve Rotation section of this repair procedure be performed.

2. Clean and mark the tip of each exhaust valve stem with a paint marker. The paint mark will be used later to assist with determining if the exhaust valve has been rotated 90°.

3. Bring the #1 cylinder piston to top dead center using the mark on the crankshaft front dampener/pulley. This step is important to prevent the possibility of the exhaust valve from falling completely into the cylinder.

4. Install the essential service tool valve spring compressor, MD-998772A, to the #1 cylinder exhaust valve spring.

Note: The following valve rotation procedure was developed with the use of valve spring compressor tool, MD-998772A. The MD-998772A compressor engages the entire perimeter of the valve spring retainer, unlike other make valve spring compressors.

5. Compress the #1 cylinder exhaust valve spring enough to gain access so that the exhaust valve can be rotated 90°. Rotate the exhaust valve 90°. Slowly remove the compression on the exhaust valve spring. Verify that the valve keeper is properly seated to the valve stem and valve spring retainer.

6. The 4.0L firing order is 1 - 5 - 3 - 6 - 2 - 4. Without rotating the engine crankshaft, repeat steps 3 through 5 to cylinder #6.

7. Rotate the engine crankshaft 1200 and repeat steps 3 through 5 to cylinders #5 and #2.

8. Rotate the engine crankshaft another 1200 and repeat steps 3 through 5 to cylinders #3 and #4.

9. Install all cylinder rocker arms (intake and exhausts) and retaining bridge. Make certain that the push rods are properly seated to their respective rocker arm and lifter. Tighten the respective cylinder bridge/rocker arm cap screws to 30 Nm (21 ft.-lbs.) when each cylinder piston is at top dead center (cylinder intake and exhaust valves are closed).

10. Install the engine cylinder head valve cover. Tighten the valve cover bolts to 10 Nm (85 in.-lbs.). Refer to the appropriate vehicle service manual for detailed assembly instructions.

Decarboning Combustion Chamber and Valves:

1. Start the vehicle’s engine and allow the engine to reach normal operating temperature.

2. Remove the air tube from the engine throttle body.

3. With the engine at idle, spray the entire contents of Mopar Combustion Chamber Cleaner, P/N 04318001AB, directly into the throttle body. As the cleaner is being ingested, allow the vehicle to “load up” with the cleaner to the point that the engine is almost stalling out. Maintain this condition until all of the cleaner is used/ingested.

4. Stop the engine once the entire can of cleaner has been ingested.

5. Install the air tube to the throttle body.

6. With the hood closed and the vehicle parked inside the garage, allow the vehicle engine to heat soak for two to three hours. This will ensure that the engine will maintain its temperature and will allow proper solvent penetration.

7. After engine soak, start the engine and drive the vehicle until the engine is has reached normal engine operating temperatures.

8. If the vehicle is equipped with an automatic transmission, place the gear selector into “L” (low). If the vehicle is equipped with a manual transmission, place the transmission into first gear.

9. In a safe vehicle operating location that will allow the vehicle to be driven safely and at the posted speed limit, accelerate the vehicle until the engine reaches 4,500 rpm.

10. Hold the engine speed at this rpm for 15 seconds.

11. Slow down and in a safe location pull to the side of the road. Allow the engine to idle for five seconds.

12. Repeat steps 9 through 11 five more times.

13. With the vehicle at operating temperature and using any available freeze-frame data recorded when the misfire DTC occurred, verify that the misfire condition has been corrected.

14. Erase any engine DTCs once the misfire condition has been corrected.

Technical service bulletin courtesy of Mitchell 1.

For additional information, visit www.mitchell1.com.



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Check it out.  I am taking my cylinder apart over Christmas Vacation instead of remodelling the Laundry room.(WHo wanted to do that anyhow!!!)