Well after a really thorough look at your pictures I've got some observations and I could be wrong cause the glare may be causing me to see things that are not.
two rod caps picture, that upper cap in that picture, can you confirm to me if that is the rod on the RIGHT SIDE of journal? the lower rod is LEFT side of the pair? I'm guessing but I have suspicions based on the marks in the bearings and on the crank.
It appears the bearing on the upper cap in picture is starting to fail and is wearing through to the copper layer.
Again this is just an educated WAG

if such a thing exists. Suppose that's like Microsoft works or jumbo shrimp...an oxymoron?
I won't say for certain however my suspicion is that at some point some bit of crud was picked up and passed through the oiling system, or the filter's bypass opened up and allowed some unfiltered oil to pass through system.
The other thing it could be was a burr on the cranks oil journal and may need some light champhering, again with no real good image of that spot yet, it's supposition.
Crank looks ok and likely will get by with a good micro polish, I'd not be grinding it as it has a hardened surface. Look for a replacement crank if fault is found that warrants it.
Main cap could have been machined just off square by looks of things as Gary mentioned align hone would be nice.
Again untill the whole enchilada is there to see it's difficult to say. Doing things right the first time when this deep in can mean the difference between 10000 mile ??? engine and 200K+

engine!
Keep the pics coming and we will surely keep the commentary up too.
JM2CW take what ya want...leave the rest.
Al