I like how you reflected about potential problems as you went ( nest boxes may be too high, I'll lower them if they are).
I am concerned that you used chicken wire on the windows and the upper part of the run. Raccoons are good climbers and can easily tear through chicken wire. I would suggest welded wire or hardware cloth every where you put chicken wire.
I like your small shelf for germx and how you have your cleaning implements hanging on the wall within easy reach.