2000 Jeep Cherokee 4.0L Misfire with Flashing CEL: Diagnosis and Fix Guide

The 4.0L engine in older Jeeps is known for carbon buildup leading to pitted valves, which can cause misfires — especially in cylinder #3. If the issue persists on a single cylinder, a cylinder leakage test would be highly recommended. I've also seen dirty fuel injectors, blown head gaskets, or vacuum leaks as common causes of misfires. As a low-cost diagnostic step, you could swap the injector from cylinder #3 with one from another cylinder (not adjacent) and retest to see if the misfire moves. For the 2000 model, is it the large central ignition coil? Does it have separate wires or just a single rail?

Yes, the 2000 Cherokee has a long, centralized ignition coil with no individual wire harnesses — just one main coil connected to all cylinders via a distributor-style rail. I recently noticed my valve cover gasket is leaking, which is common in Jeeps of this era. Could a leaky valve cover be causing pressure loss and contributing to misfires or poor idle? Worth checking.

No — a leaking valve cover gasket is unlikely to cause a specific cylinder misfire like the one in cylinder #3. The issue appears more likely to be electrical or fuel-related, especially given the recurring nature of the problem after plug changes.

Turns out it was a faulty ignition coil. I took it to a shop for diagnostics — they ran tests and charged $130. They tried to charge an additional $400 for an OEM ignition coil and installation, but I went back to Advance Auto Parts and replaced the coil myself. New question: I’ve heard that Autozone has better parts than Advance. Are there real differences? Or are both just low-quality aftermarket brands? What about O'Reilly's or Napa? Which is best for reliable aftermarket parts? Thanks, Jeff Compton — and everyone else who helps!

My experience isn’t based on Autozone vs. O'Reilly’s since we don’t have either in Canada. As an aftermarket supplier, I prefer UAP or Napa because they cater to professional shops and tend to offer parts that meet OEM standards. Stores like Autozone or O'Reilly's are fine for tires, filters, fluids, and brakes — but many of their electrical components (like spark plugs or oxygen sensors) are poorly tested and don’t match OEM quality. I’ve seen numerous aftermarket ignition coils, distributor caps, plug wires, and fuel pumps fail right out of the box. This is especially concerning when a vehicle is diagnosed correctly but the replacement part fails — leaving users thinking they misdiagnosed their issue. For example, I've personally seen aftermarket ignition coils in Dodge vehicles lead to PCM (powertrain control module) failures. Your situation — where the engine runs fine for days then suddenly returns to misfiring — raises questions about both diagnosis accuracy and part quality. It’s not a 'Bosch vs. others' debate — I’ve had issues with Standard, Bluestreak, and other brands too. The best aftermarket parts are those made by the same OEM supplier as original equipment (e.g., Bosch O2 sensors). If a cheaper version of a Bosch sensor were just as reliable, GM would have used it from day one. The reason it’s not is because such parts don’t perform reliably long-term — they fail before warranty ends. Ultimately, I recommend dealer-installed parts for critical components like ignition coils or O2 sensors. Dealers know what's actually needed and can provide updated versions of parts if available. For example, a Ford EGR valve might be mislabeled as an 'EGR' when it’s actually a DPFE — a shop trained on Ford trucks will recognize this. A store employee at Autozone might sell you the wrong part because their code reader suggests it. I trust professionals who work with vehicles daily over those who only handle parts part-time.