You asked about what goes on top of the crush/run, in our stable we have the crush stone and then they put a mesh barrier then rubber mats. The mesh barrier looks like the kind of mesh used for grass reseeding. Any liquids seep into the crushed stone, and the pine shavings stay in place and dry quickly. I use sweet PDZ horse stall freshener sprinkled through out for smells, and we have a 3 inch deep poop deck filled with sweet PDZ that I scoop daily--No chicken smell--the ammonia gas is broken down instantly and you can use it in your cats litter box, under for clumping litter, on top for non-clumping.
It may be a little late but I'd watch the tops of the block and the bottom of the shed walls for rot, usually you would put a moisture barrier along the tops where it's in contact with the walls.
I think you got a marvelous coop, your girls should settle in better when they leave the "teenage" months.