That is really nice!!!
You said you were going to make nest boxes and put them on top of their little houses.
I think it might be better to do something else. As you already know, they like to hang out on top of their houses, and chickens like to roost high and lay eggs low.
I think they will lay in the little houses. You didn't show the inside of them, but can you make a nest area inside?
If you put nest boxes on top, I think they will roost there, and create a nice mess for you to try and keep clean.
Just throwing this out there, since you asked. Something for you to think about.
About the coop, pens and run...I think you did a fabulous job! Very well thought out, practical, and safe for the birds. I really like the run, so you can let each pen out one day at a time to play and run around while being safe.
Jean