Old thread but fairly recently renewed I see. I had a very similar problem a few months ago, and it had a different (but ultimately very simple) cause. Long story, so skip to the end if you like.
Engine running a little hot, marginal exhaust gas reading in the coolant, 0331 head (2001 XJ). Probable small head gasket leak, but as long as it had to come off anyway for the gasket I had it replaced with a new casting from Clearwater. Also had some other work done (I'll get back to that). Two weeks later I took it in for a smog test, and it failed badly with high NOx reading (Southern CA, required to use a test only station). At 15 mph I measured 1062 ppm (max 517), while my previous high reading in years past was 5 ppm. No OBD code thrown. Brought it to a gold shield repair facility (now STAR - call it #1), who initially diagnosed throttle body shaft air leak using a smoke test. Those were on national back order, but I found replacement bearings (actual bearings, not bushings) from Hesco in Alabama. Replaced, but no help. They drilled a hole in the exhaust pipe just before the main CAT (which is the only one that reduces NOx BTW) for an intrusive test and determined that to be the problem. New main CAT, but no help. Next step they said was the two pre-CATs. They are expensive ($1400 just for the parts), and dealer only - no one else makes them, and you can't buy them used (illegal, so I'm told they get recycled first thing at junk yards).
Finally took it to a different shop for a second opinion - Phil's Auto Clinic in Hemet. I can't say enough nice things about that guy. Phil diagnosed the problem quickly as a leak in the exhaust pipe between the manifold and the CAT. Matter of fact, that's where I'd had a short piece of flex tube inserted at the same time the head was replaced (I said I'd get back to that). The intention was to isolate vibration and maybe forestall a cracked manifold, which I'd read was the other problem (besides the weak head) in 2001 XJs (I also upgraded to Brown Dog rubber engine mounts at the same time for the same reason). Took the Jeep to a muffler shop around the corner from Phil's and for $30 had the flex tube welded on. Back to Phil's and now I passed emissions test.
Back to the test only station for final retest. I was passing, but not nearly as well as I used to. Back to gold shield repair shop #1, and I had them get my OEM main CAT back before it was recycled, and I figured it was probably better quality than the aftermarket I had on. I had them put that one back in (technically a no-no as it was used, but only by me). Still passed, but actually a little worse. I stopped there. Not happy with the emissions, but at least it passes.
A few weeks after that it started running rough and throwing a code indicating a misfire on cylinder 5. Back to the original shop that replaced the head, and they found the exhaust valve burned (pressure test and boroscope examination). Clearwater has a warranty that would probably have covered the head, but I had to send it back to Florida for them to examine, and they would repair or replace at their discretion. They were actually very nice, but they thought the problem might be the E10 fuel we use in CA. I could buy a new head, but then I'd end up with two. My XJ is my daily driver, and a rental car would have cost more than the head. I had it rebuilt at a local machine shop (who said everything except that one valve looked fine) and paid for a second install (it wasn't the fault of the original installer). Tappets looked fine BTW. In retrospect that valve may have been increasing temps and contributing to the high NOx reading, which is why it's part of the saga.
So, after all this I was still running a bit hot, especially when stopped at a light after getting off the freeway (whoever came up with that name anyway) or coming up a hill. I replaced the fan clutch with the NAPA 272310 one a couple of days ago. And that was the easiest and best upgrade ever. Stays between 195 and 210 now, and it fit right in (without tilting the OEM radiator or even removing the electric fan). The part seems to have changed a little for the better since others wrote up about it though. No longer has four protrusions aimed at the radiator, and it seems quiet to me (doesn't interfere with my hearing aid at all). The central core is now thicker so I couldn't get a gearwrench on there to tighten the nuts on the studs, and I had to use an open end wrench and a bit of patience. And a telescoping light and magnet to retrieve dropped parts - gravity can be so annoying.
OK - for everyone who skipped to the end: look for a leak, even a small one with no noise, in the exhaust pipe. Smoke test (shop #1) didn't see it and they said they looked specifically at the flex joint. Air gets sucked in (as well as pushed out), and that throws off the lambda calculation. Test reads high NOx, but it isn't really. Accuracy of the emission test is compromised if outside air mixes with the exhaust before the test point.
near Houston, LOL. Why?
