I don't know what the summer temps are like in your area, but I would strongly suggest screwing hardware cloth over all the windows from the inside - it's easy to do if you use screws through large washers - your shutters will still close that way, but they can safely be left open in warm/hot weather. The area that you mentioned using as an egg door in the future: I would add hardware cloth across the bottom section if that opening I see is large enough for a raccoon to stick an arm through...
Since your entire coop/run is a rectangle shape, it'd be very easy for you to add a wire skirt of 12 - 18 inches around the whole thing. Just lay a strip out flat on the ground next to each straight edge of your coop, overlap an inch or so onto the coop or the run frame and screw it on using washers on the plastic part and the U shaped nails on the wood part. That discourages digging predators, because they're digging on wire rather than dirt.
Also, know that chicken wire (at least I think that's what you're using) is great for keeping chickens in or out of places, but is not very strong against dogs, raccoons, etc....
Since your entire coop/run is a rectangle shape, it'd be very easy for you to add a wire skirt of 12 - 18 inches around the whole thing. Just lay a strip out flat on the ground next to each straight edge of your coop, overlap an inch or so onto the coop or the run frame and screw it on using washers on the plastic part and the U shaped nails on the wood part. That discourages digging predators, because they're digging on wire rather than dirt.
Also, know that chicken wire (at least I think that's what you're using) is great for keeping chickens in or out of places, but is not very strong against dogs, raccoons, etc....
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