So the jeep started running ruff, like missing. There were no codes at first but the finally came on. It is showing 12, 11, 47, 21, 43, 43, 55. I take it the 43 is missing fire. Looked at some of the other codes and 47 seems to be low voltage from the alternator. Could the other codes be from low voltage?
It is a 96 4.0. I have in the last 8 months replace camshaft, crankshaft position sensors. I check the cap and rotors they were replaced not long ago. I did replace the plugs. Just champion copper The old ones looked OK. I am guessing at pulling the alternator and getting it tested.

 

As you have a 96, you can get more detailed code information by using a code reader or a scan tool to pull the full P0XXX code. These full codes provide more direction than the two digit codes that you listed which I assume you retrieved by the "key on, key off" technique.

Start there. Post up what codes you find. With snaky problems like you are describing, you want to use OBDII to the fullest of its potential.

Good luck and keep us posted!

 

Well now, lets get back to basics. Is it running rough at idle, speed, or all the time? Does it ever smooth out? If so, when? When you had the plugs out did you inspect them carefully deep inside or a cracked porcelain insulator? Are the plug wires touching anything? Look carefully in the cap for any cracks. Is it missing on a regular interval like it might be a bad wire or plug? I've (twice) had a nearly new spark plug fail internally and chased all over the place for the 'miss' and didn't find it. Eventually did, but who'da-thunk it to be a new spark plug? So if it's a regular miss, I'd almost start with a compression test then work back through the ignition system. Check all connectors and injector connectors too.

Then go to the vacuum side: Does the 'miss' change at all when you tap the brakes? Do you hear any 'hissing'? Inspect the vacuum hoses carefully. What vacuum are you pulling at idle and 1200 rpm? Check the PVC Vacuum and any hoses or lines from the PVC system. I had a plastic line and the rubber elbow was cracked on a vehicle. Thing is, you couldn't see it.

With the computer, the IAC could be plugged, the throttle plate could be gummed up (common), the O2 sensor or temp sensor could be flaking out...lots of things. I had a bad temp sensor on my pickup and it ran fine till it got cold. Reason is, it had 'drifted' but only when it became colder did the ECM notice the drift at out-of-spec. You can measure ambient temp and check against a resistance chart (before you start it).

Start with the simple things. On our 03 GC I had all sorts of unrelated codes from a simple EGR leak that had me chasing my tail all over the place. Eventually I just had to do basic inspection and troubleshooting. Sometime it can be multiple issues which compound things. Sometimes the computers can give non-relavent codes. Check some things out and tell us what you found..

 

I think there are some 96s that ODB2 does not work. Every scanner I have tried does not work.
When I pulled the plugs they all look OK for 9000 mIles on them. I pull the alternator and it tested good. I checked wire connections and the vacuum lines they seem to be OK. Cap and rotor still look good no cracks or build up.
It started out when I would start up and try and give it gas it would start to sputter and then clear up. Now it sputters once in a while at idle and it may clear up but seems to be getting worse.
I will have to get a compression tester and test it and the fuel pressure as well while I am at it.
This jeep sat for 2 years in a farmers field. I had to replace almost all the sensors to get it running and some trans work. New exhaust, brakes ect.
I did do the four hole injectors to replace the old clogged up ones. Maybe they could be a problem. i think they were cheap ones.

 

The fact that this vehicle sat for two years is for sure a wildcard.

1. Job #1 absolutely/positively is to ensure that you have a good (new?) battery and that your alternator is charging it properly. All automotive electrical life starts with a good battery and that it is being charged properly! Electrical gremlins can cause weird codes and result in the chasing of your own tail. One of your codes deals with low voltage. Have your battery load tested (any parts store will do it for free) and put a meter on the battery, while running and at a high idle you should see approximately 14.4 volts to do a rough test on whether or not your charging system is up to snuff. Do not troubleshoot any further until you are sure about the electrical performance of your XJ.

2. While there are a lot of other possibilities, and if the battery and charging system check out, then I would test fuel pressure. Start with the basics and nothing more basic than fuel pressure. 96 was a year of change for the fuel system on the XJ. Early 96 had the regulator under the hood and for those, fuel pressure spec is 31 psi. Then disconnect the vacuum line leading to the regulator and pressure should jump to approximately 39 psi. For later 96 Xjs, the fuel pressure spec is 49 psi, plus or minus 5 psi.

3. Performing a compression test is never a bad idea. A good "snapshot in time" on the internal condition of your engine. The spec for the 4.0 is 120-150 psi, with no more than a 30 psi variation between cylinders.

Hope this helps. Good luck and keep us updated!

 

Well it looks like it is some bad cables. After putting the alternator back in to take it to work to check compression and fuel pressure. It is running fine. It looks like it time to up grade the battery cables. The volts are staying higher now and not dropping as much.