Looks really good. Too late to help now, but on the roofing nails, most of the box stores sell them in shorter lengths than the basic lumber yards do.......I'm using 7/8" roofing nails on 5/8" plywood roof decking and they are not breaking through. I'm not sure why folks use the longer ones in the 1 1/2" range, unless they have fat chubby fingers and need the longer nails to keep from whacking their thumbs. Once it breaks through the decking, it's not holding tight to anything and it does represent a hazard to navigation when you are inside and beneath the decking.
Two options on adding more ventilation. Simple gable vents if you need some size. But also consider a round dryer vent......the type with a plastic pvc cover with a grid screen. It will be about 3" or so in diameter. Drill a hole in the side up high near the peak........and screw it in place. Put one on either side if you need more.
There is another aspect of "chicken math" that most are not aware of, and that is the factor of size of the coop. A 4' x 6' coop does not sound all that much larger than 4' x 4', but is 50% larger. A 6' x 6' is 2.25 x larger.......so you go from 4 birds to 9. And square gives you more interior volume per linear foot of wall than a rectangle does. So square gives you the most bang for the buck.