It doesn't go away, per se, but sometimes it seems quieter after it's been running for a bit. The reason I am thinking flexplate is that the sound goes away under load or with higher RPMs, which I've heard is typical of a cracked flexplate, but I'm not sure. Wouldn't bad pistons or bearings get louder or at least stay the same with acceleration?
Whoa! You did all that with the engine IN the Jeep? I was looking at the oil pan the other day and it looks like I will have to remove the exhaust to be able to drop it, is that correct? anything else you needed to remove that I can't see yet?
Here's a quick video of the sound while revving the engine: