I was really hoping that would be the case, and if a few scratches and pits remain, that is OK. I would normally want to get them all out with a fresh bore, but 340 blocks are reputed to be more problematic as to how far you can bore them, as their bores start pretty big to begin with. And over .060" would be .080" and new pistons and that cost, and the bores might just not take it. I would want to run it as is and get what life I could out of it. If you want to run it on the street for a while, then ask them to hone it the least they think they can get away with for a good ring seal, and let it go at that.
(Just do your best to get any loose rust particles out of any pits; iron oxide is an abrasive.)
The point on the piston order is that it does not matter. These pistons do not have what is called 'pin offset' and so don't have the notch on them that indicates what side of the piston points to the front. If they had notches then you would have to keep them on the correct side. You can mix and match these as you see fit. For lack of any other reason, I'd put the shortest rod and pistons sets up front, where the deck looks to be the shortest. Just make sure that the oil squirt hole is aligned in the right direction on each rod with the piston eyebrows 'up'.
And spend some time after it comes from the shop to clean, clean, clean, the block and crank. There could well be some grit and cam bits left despite their cleaning efforts.