When I got my 84 CJ with the straight 6, after about 80k I developed a knocking noise. It sounded like a rod knocking. I was scared to drive it so I had it towed to a shop to check it out.
When they got it and started it up the noise was not there and they could not find anything wrong with it.
I drove it home and didnt hear it again for some time, but it did come back for ablut 15 minutes and then gone.
After talking to several jeep owners and posting on forums. Someone told me that there was a issue with the cam slightly moving back and forth and would hit the back or timing cover of the head causing a loud knocking noise and would not do any damage to the cam, so I left it alone.
I put another 40K on the engine and didnt have any issues.
I then sold the engine and swapped a 355 SBC into the jeep. The guy that bought the 6 never came back to me with a complaint about noise.
Don't know if this is something your experiencing but just thought I would post it.