replace rear main= knocking?

Why have I heard so many different stories of people changing out the rear main seals and the motors than begin to knock? There is a local Jeep specialty shop and they won't even do the rear main service without having the customer signing a waiver that the shop isn't liable.

after a little research sounds like its an issue of torque, that no 7 (i believe) cap is the one that comes off and it needs to go back to 80 ft lbs i think, from what is being talked about in this thread it sounds like his problem was the main cap bolts were backing out, if it were mine i would do it but loc-tite the bolts good and let it sit for awhile and not run it immediatley, running it out won't let the bolts settle and stretch to where they will sit under load.

read a recent post that a new oil pump was hitting the side of the pan and once it was repositioned the knock went away

Jess said:

read a recent post that a new oil pump was hitting the side of the pan and once it was repositioned the knock went away

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ya i saw that but some of the others were spinning the crank bearings because the torque was off. If my rear main were leaking bad i wouldn't hesitate to change it just make sure that the bolts were given time to stretch under load before firing it up and driving arund the block

I have heard multiple stories of it doing it without replacing the pump. Before I consider doing this I want to know what to avoid.

I've never replaced the oil pump, never had any issues. But I have had the seal start to leak again in fairly short order, like a few months. I've changed the same seal on numerous occasions, never noticed the rear main bolts being loose, I probably would have noticed when I removed them again.
I typically clean the bolt and block thread holes with brake cleaner and add a dab of blue Loc Tite. And torque to spec., the Loc Tite likely acts like a thread lub and the actual torque is increased a bit.
I have had issues disturbing the junk that builds up inside a motor. Some of it is jelly like. The oil passages aren't that large and my oil pressure has done odd things for awhile, like too high and a jumpy needle. It all seemed to eventually work itself out after awhile. But it always made me nervous. I do clean up the pan good and do the best I can with the oil pump pickup.
One of these days I'm going to remove the pump and check the clearances. The oil pump gear teeth have never shown much wear on the 4.0 pumps I've looked in. I get the feeling most of the wear is on the gear sides and possibly removing the pump gasket and replacing it with a thinner one, could increase efficiency. The oil pump regulator (or pressure relief valve) spring has to be suspect. Over the years the spring has likely relaxed a bit or the valve has gunked up.