I see its elevated with a solid floor so you don’t need to worry about something digging into it, but if you add a run, I’d suggest you look at the apron method for the run instead of trying to dig down in that soil. That’s probably real rocky and you’ll likely hit some tree roots. Just lay maybe 18” to 24” of that welded wire flat around the outside of the run, attach it really well to the bottom of your run, and cover it with a couple of inches of dirt or rocks. The idea is that a predator goes up to the fence, starts digging, hits the wire, and doesn’t know to back up. It’s effective and a whole lot easier than trying to dig down.
A lot of people really like those fender washers to hold on the hardware cloth, but I use wood lathing instead where I can. Take a strip of wood two or three inches wide and maybe ½” to ¾” thick and screw that on top of the edges of the hardware cloth. Pre-drill the pilot holes so you don’t split the wood and put the screws through a hole in the hardware cloth. That holds as well or better than the fender washers, doesn’t give the raccoon an edge to pull on, and keeps the sharp edges of the wire covered so you don’t snag your clothes or hands on them.
As a minimum I’d keep the tops of the walls under the overhang open and covered with hardware cloth year-round. That will provide ventilation and keep rainwater out. A roof vent or gable vent up high wouldn’t hurt a thing but I’d not do a ridge vent. Snow could block it where you are. Just keep the roosts low enough so they are lower than those openings and the birds will be below a cross wind. Close the windows in the winter but open them in the warmer weather. I don’t think you need flaps on anything above their heads unless you run into a “rainwater getting in” problem.
No coop is going to be 100% predator proof. The more you spend the closer you can come. And your building techniques come into play. You have to attach the material so it will not come loose and you have to have solid enough material it can’t easily be smashed. A hot wire is about the only thing that will stop a bear but hardware cloth properly attached will stop most things you are likely to see. I covered my window with hardware cloth and have been happy with that. If you want to be even safer add a layer of that welded wire over it.
It looks solid and well-built. I have some issues with it being raised like that. The chickens can probably get back under the coop from what I can see. If one starts laying under here or is hurt and you need it retrieve it, how do you get to it? If you block the chickens out of it, that becomes a great place for mice and other vermin to nest. That could become a place for larger animals to den. You probably can’t do anything about mice and such other than maintain a trapping program, but I’d give real serious consideration to blocking that off underneath so bigger things can’t get under there. I know why you did it that way, the ground isn’t level so you solved that problem. There are always trade-offs.
I think it looks really good and well-built. I think you’ll be happy with it. Good luck!