look as though you have some very good help
glad you joined us many will always volunteer help others like you are smart to ask questions... looks like you are well on way 


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...Can always use pieces of cardboard tacked up inside to direct any breezes upwards instead of right onto roost area....
I didn't even begin to think about keeping rain from getting in the vents. There is MAYBE 2"-3" of overhang all the way around. If I do the vents up high on front and back like you suggested I don't think I'll need to worry (especially with the bit of tree coverage in back). But plexiglass is something I'll need to invest in for the sides (or just keeping the wood when I cut the holes). The right side is where the wind blows from and so it'll be the side I need to protect most. It'll also be the side that the run is built on though and I plan to add a roof to that.