Hmmm...I have yet to master mind the internals of a 4.0 because the deepest failure I had was needing to replace my intake. However, I have a Subaru Legacy that I have diagnosed with a bad timing belt. I ran the engine with timing cover off and observed the belt, it was jumping a bit and quite loose. It has however driven 3000 miles since then with no power issues or anything, great MPG, smooth idle. The noise in your video is so identical to the sound and rhythm of your Jeep. I was able to pry on the failing hydraulic timing tensioner and when I applied manual tension, the noise cut out immediately. I don't know if a 4.0 can be ran with a simple removal of a few bolts like a subie cover, but when your watching the engine run with the cover off, wherever a tensioner is, if their is a way to simulate full tension with a screwdriver or something, see if that correlates to the noise going away. Otherwise, ground the cylinders one at a time and see if any certain cylinder being cut out removes the knocking/slapping noise. Try a stethoscope from an auto parts store and probe around for an area where you hear it most. Do a compression test, pretty easy. Valve cover is easy to remove also, then you could atleast do a quick visual inspection for anything obvious valve related, and also have a good opportunity to replace the cover gasket.