I have a 2001 Cherokee that I have had since new. At about 60K miles the engine started to make a noise similar to a clacking sound. Its not super loud, but noticeable. The best way to describe it is that it sounds almost like the older diesel engines. I went through a myriad of items inside and out trying to track down what it was, including most of the issues that are regularly mentioned here. I never really found the issue. Power and performance were never affected. One day, quite a few years back, I was talking to a Jeep friend at a Jeep dealer and told him about it. He said that he had heard about 'that 4 liter diesel sound' from others, as well. He went and got an old guy from in back. Turns out this old guy used to work at an AMC shop way back before Chrysler took over. He said he had heard off and on stories of the same damn noise coming from not only the 4 liter engines, but also from the 4.2 liter engines which were made in the years before the 4 liter came to be. Mechanics always attributed the noise to loose tolerances in the engine, as compared to others. He stated that years back, it was explained to him that the 4.2 liter engine, and later the 4 liter engines, were never designed as a high quality, tightly built engine. Looser tolerances allowed for faster machining, and therefore faster assembly at the engine plants. And much of the dimensions and tolerances of these engines have not changed over all these years, they have quite an interesting history if you get to reading about their begining. The engines ran well and appeared to be tough, but some of them, after acquiring some miles, started to chatter. But it never turned into anything serious. They can just be noisy engines sometimes. Im not saying there ISNT anything wrong with your engine, there may be and it would be wise to do a thorough investigation. But after doing my investigation years back, covering almost every aspect you could think of, the sound is still there. But my engine is also up to around 220K miles now, and still runs really damn well. And Im not exactly easy on the 'ol girl either. All's I do when the topic comes up or someone asks about the noise, is shrug my shoulders and say that it runs great!
