Windows: You can NEVER have too many.
Hardware cloth on any and every interior surface unless you don't mind mice (or something worse) getting in. Mice will chew holes in the wood, and eat/pee in/poop in the feed. If they do, and the birds don't eat them, chipmunks and/or rats will follow, and then weasels are sometimes not far behind. Vinyl flooring makes coop cleanouts easier than pretty much any other flooring surface: Just sweep dirty shavings onto a tarp outside the door, and drag tarp to wherever it's going. Non porous and no seams means fewer places for bugs to hide and breed, and it can be mopped if you wish. Definitely make roosts removable, or a one-piece ladder type that can be moved out as a whole: if not, no matter where you put them, they will manage to get in your way at some point.
No matter where you put your nesting boxes, how you design them, how many you put in or what they look like, everybody will likely just use one (or two, if they can't cross their legs any longer) so don't waste a bunch of time putting a lot of thought into them LOL! Upside down plastic storage tub with a door cut in the end is the current hen favourite (of the cooped birds) at my place, and bonus points for being scrubbable.
If you can put a small roof over hatch openings, do so...snow and ice can get in there in winter and stick them, and for some strange reason, birds get upset when you beat on the doors and frames to unstick them

Don't: use spray foam insulation anywhere, for any reason, unless you sheathe it in with something bulletproof. The chickens will just eat it.