Had a unknown squeal-type problem with my 94 YJ which went on for about 9 months starting at the beginning of 06. Was hugely and annoyingly noticeable at idle; exhaust noise may have masked it as revs climbed. But, urban driving in this Jeep was a nightmare until the problem was found last month.
Originally thought it was coming from the intake area, which, in the end, wasn't too far off. Looked at the 4.0 TB I had as the cause of the noise - no deal. Swapped out the Spacer for one with no swirly deal - nope. Decent Burbank, Ca. 4x shop spotted a bad fan clutch - that didn't fix the noise though. Finally picked up a Sear's mechanic's stethascope - but everything sounded great through it. The squeal noise :sad: persisted.
Only area I couldn't get to with the stethascope was the water pump area (due to squeal noise being an engine-operating thing, which made getting to the water pump with the stethascope, challenging). So, I upgraded the waterpump with a Flow-Kool - this didn't fix the squeal, but at least I got a better pump out of the unnecessary fix.
Anyway, when all was said and done, it took a team of 3 mechanics almost an hour to track the noise. Turns out it was due to a bad intake/exhaust manifold gasket. Apparently there was damage in the gasket at the underside of the intake manifold, which made tracking the damaged gasket area, visually, challenging. The mechanic that found it literally had to put weight on the intake - only then did the squeal noise change pitch - which tipped the guy off to the problem. In 20 years of owning cars, that intake squeal problem really "took-the-cake" in terms of giving me an engine problem I, or a lone mechanic, couldn't figure out in short order.
If you have a squeal, have checked out everything running off the accessory drive belt, no vacuum leaks anywhere, then get the intake/exhaust manifolds checked out and the gasket checked out too. That did it for me. Also take a look at TB area, especially if you've upgraded to a 4.0 or use a spacer - these areas are prone to cause noise too.
Have to mention that the intake/exahaust gasket and leaks/noise there weren't talked about much in any jeep-related google searches I did. Most of the suggestions there towards solving my squeal noise problem tended to run towards replacing the belt or accessories, the TB, the spacer etc.
Also, should mention that if you have a high mileage 2.5 (well-maintained or no) you are probably going to see this kind of wear on the gaskets, maybe more so if you are twisting o pounding your rig alot off-road.
Good luck :D