Hi tJKrider,
I had a similar problem with my 2010 JK Rubi at about 135,000 miles. Mine has the 3.8L EGH V6 so your 3.6L Pentastar may be different. But here's what I found:
In my case there were several issues that all contributed to the problem. The most significant was the bearing in the water pump. It was failing and it was making most of the noise. But the idler pulleys contributed a little. And the spring in the belt tensioner had lost some of its strength and allowed a small amount of belt squeal. So I replaced all of the parts with original Mopar parts and my engine sounds like new.
In your case, it sounds like you've replaced everything except the water pump. In my case, it was the part that created most of the problem and it was intermittent just as you described.
I'm so glad that the water pump was failing slowly and loudly. I've been driving Jeeps since the CJ days and have had quite a few. I had to replace water pumps in several and, in all prior instances, the water pump failed suddenly and totally. So I had to immediately stop and have my Jeep towed home so I could fix it. I'd hate to have a water pump fail while I'm a long way from home on a trip. So I'm grateful that my JK water pump made the noise before failing completely.
Whenever I take a big trip out west where help will not be immediately available, I take a few spare parts and tools in case I need to fix something like this. A spare water pump is now part of my repair kit.
Tips: On the 3.8L engine, the water pump mounts to the aluminum timing cover. If the water pump on your 3.6L does, also, beware of the timing cover's fragility. It is very easy to damage the soft threads of the water pump bolt holes. And, since the water pump bolts are steel, there will likely be galvanic plating that may make the bolts difficult to remove (many DIYers report breaking a bolt or two). So, before you remove the bolts, soak them for several days with some good-quality penetrating oil. And do NOT use an impact driver to remove or install the bolts. When I did my job, I replaced all of my water pump bolts with new ones made with harder steel. This is such a common problem that aftermarket companies sell extra-hard bolts for Jeep JK/JKU water pumps. And use some anti-seize compound on the bolts when you install them. The anti-seize compound will protect the bolts from galvanic plating so the next time you need to replace you water pump, the job will go a lot easier. I also added a thin bead of liquid seal compound to both sides of the Mopar water pump seal where it contacted the pump and the cover. That way I would be sure of a good seal. Finally, be sure to use a torque wrench when you tighten the new bolts. You cannot use much torque because of the soft aluminum metal of the time cover so you must be careful not to overtighten. But, if you use anti-seize compound, you will need to add maybe 10-20% more torque. The torques for the 3.8L engine are 12 N-m / 9 ft-lbs / 105 in-lbs for the 10 mm bolts and 28 N-m / 21 ft-lbs / 250 in-lbs for the 13 mm bolts. You'll need to look up the torque settings for your 3.6L Pentastar.