[DSXMachina]

Great thread, subscribed! Love to tear engines down, and love it even more when someone else is doing it!
I'm a latecomer to the thread, and did read all 10 pages but don't recall discussions in regard to two points. First, it looks to me that the chunk which is missing out of #5 slug is actually melted out due to blow by in an area where heat concentrated. Second, on that same #5, are the oil rings free? The compression rings obviously are but the scrapers look stuck in place.
It also looks like what you describe as scoring is very unusual. Normally I would expect to see more of the cross hatching gone in the same vicinity if it were the kind of scoring I am used to seeing. My theory is that you built up guck and micro particles on the oil rings and they transferred abrasion over to the cylinder wall. Look closely at the cylinder pics and you will see that the black varnish extends down to the level of where the oil rings are. This is much lower than usual, it ends at the uppermost compression ring in my experience.
Is the block going to be bored? Or just honed? If honed I would have to call them scratches and not scoring.
I have a theory in regard to the valve stem deposits, I am still thinking it through.
I've enjoyed the civil discussion in this thread, with its very knowledgeable contributors.