I'd pull the pan take the connecting rod caps off (mark them for position and direction). Visually inspect the bearing. Look at the top bearing also. Not hard to raise the piston (spark plugs out). You can inspect some of the cylinder wall for scuffs. Plasti gauge all the connecting rod bearings top and bottom. Check and see what is in the bottom of the pan. The hardest part is getting the pan off and cleaning the bottom of the motor. I use half a dozen cans of brake cleaner and let it drip over night. Check the side of the block, distributor side, for the codes for off size bearings. If you replace the connecting rod bearings, too tight is worse than a tad loose.
Even after all the work and you still have a knock you will at least raise the oil pressure 50%. With a T type cylinder mic you can do a decent measurement from the bottom and get an idea of what you have for cylinder wear. I've seen some sorry looking main bearings work just fine, I don't mess with them unless I'm doing a complete rebuild. Connecting rod bearings with black scorch marks means you have an oiling issue, worn through the coating in places is normal, scoring has to be severe to be an issue. IMO the 4.0 is pretty forgiving and was designed to last, not for race car tolerances.
Side note I've found some connecting rod bolts that were pretty darned loose, not much tighter than finger tight, always made me say Oh wow to myself. I've also found two number three caps in one motor, that was kind of a head-scratcher.
What is your oil pressure like, a mechanical gauge not a dash gauge?