Looking good so far! Why dont you want the nest boxes under the droppings board? And another idea would be to leave the milk crates under the window and put some sort of a roof over them to protect from rain blowing in the window. Also, if you want more than the 2 nest boxes, you could put them on the floor. I don’t understand why everyone says nest boxes need to be up off the ground. Ours never have been elevated and the hens almost always lay in them. And in nature they would nest on the ground, so elevated nest boxes dont seem like a necessity to me. They would allow more floor space though, so that is one reason.
And thanks for the tip, I’ll definitely start looking for windows before I build any walls.