I recently have had trouble with my '04 jeep wrangler (4.0L). I have also been getting the run around from three different places. the first is a jeep dealership, the second is an offroad specialist (did the aftermarket work on my jeep)and the third is a popular tune-up shop. My jeep started to shake badly and erratically while idling, soon after the check engine light came on and started to blink while the acceleration quickly dwindled. By the time I got off the highway I couldn't make it past 30mph. Dealership wouldn't touch it because of all the modifications and told me to bring it to the offroad specialists. They told me it had nothing to do with the recent Banks exhaust and headers I had done with them and they suggested the spark plugs and coils might be the problem. the Tune-up place was the most helpful but not completely, they changed the plugs and coils and for a little while the jeep was ok, but still didn't feel completely right. Shortly after hitting the high-way the engine again quickly went back to it's previous problems. As for the check engine light, two places told me the codes that showed up indicated multiple misfires and cylinder 1 and 3 were not working. I've been told my next step should be to change the fuel filter. Is this plausible? should this really be my next step, or am I just on a wild goose chase, and soon becoming an expensive one at that?????  

I, too, have experienced this problem on more than one vehicle. Both times the problem for me was plugs and wires. I was told that most of the time a blinking check engine light under acceleration is due to misfire of a cylinder due to faulty plugs and/or wires, or in your case, faulty plugs or coil boots. The ignition system no longer has plug wires due to the use of coil packs. Three things will need to be checked. First is the boots between the coil packs and the plugs. Small holes, tears, or improper seating can result in arc tracking to ground resulting in misfire. If this is the case they are replacable. It is more common than most may think because these rubber boots are easily damaged if care is not taken during installation. In order to check these the coil packs must be removed. Next, check the plugs. There should be no cracks, etc on the porcelain, a misfire can result if there is. Also check for proper gap. Third check the coil packs themselves. It is possible that they could be at fault but my experience is with the first and second items usually being the problem. If you try to tackle this yourself make sure you use a good lube on the boots before you put them back onto the plugs, this will help them go on easier and help prevent damage such as tears or improper seating on the plug. Its the same lube you would use on plug wires. Hope this helps.

Mike  

Yesame

What other engine mods have you done besides the Banks header and exhaust? Cold air intake? Programmer?  

The only other engine mod is a Cold air intake. I've also kept up on the routine maintenance.  

I found another post with the same problem as you. The jeep was a 2000 with a 4L/6cyl. The fix for them was done at the dealer. Apparently there was a recall for this problem and after the dealer visit it was solved. The title of the post is "winter only misfire??". Don't know if it applies to you, but it may be worth looking into.  

The manufacturer (Chrysler) has an obligation to honor the warranty. Regardless of after-market modifications.

Your rights are protected under the Magnuson-Moss Act.

If the manufacturer can prove that the problems were caused by the after-market modification, you'll have to pay for it.

The dealer is an agent of the manufacturer and is not required by law to do warranty work. It's not their warranty. The dealer performs warranty work for the manufacturer under their dealership agreement.

So, click here and read up on your rights.

Then, contact the manufacturer rep in your area and ask them for a recomendation as to a dealer that will help with the warranty work. Let them know (politely) that you know your rights under the Magnuson-Moss Act. They'll know also and then you can get down to business.

If you have any problems, you can file a claim with the Federal Trade Commission. But, it won't go that far. The manufacturer rep knows all this.  

I must apologize to you, I was doing some reading in the sevice manual, have a vent problem, and I discovered something about the ignition system. The boots under the coil packs are not a servicable item like some of the other manufacterers. But I do agree with the above reply. If it is a warranty situation, they should repair it. Hope all works out well for you.