Reviving this thread because I have a very similar sound...
Something in the engine bay has been squeaking/squealing on and off for the past few months now. Just a couple days ago this stopped but now a knocking sound (Identical to the one OP shared a video of above) has started. I have to think that these must be related. Knocking does not start immediately when I start the jeep but maybe 20 seconds after starting. I can hear it while idiling, its coming from the top of the engine area (if I crawl under the oilpan/transmission I cant hear it nearly as well). Hard to tell if the sound speeds up when accelerating because it's too hard to hear with the engine making noise.
I have a hunch that it has something to do with the harmonic balancer. When watching it while the tj is idiling, I dont think it's spinning perfectly in a circle, kind of wobbling very slightly I think. I had it off about 2.5 years ago when replacing the timing chain and it looked to be in okay shape but it has been quite a while and many miles since then. Is this a possibility?
Any thoughts as to what it may be and what my next steps are in diagnosing? Thank you!