The hole in the run is sort of odd! I'm also not sure that there is enough space for them to get up to the roosts! You are right that the design is super weird!
I'm not a construction genius, but here are some things I might consider:
1. Buy cheap peel and stick vinyl linoleum and cover the nest boxes with it. This is significantly improve your ability to clean it--might do the floor too since it is somewhat narrow inside?
2. You might consider removing some of the wood shelf in the run...it might be nice to have one side to put your water and food on that is level and off the dirt. But chickens want the space to forage, and that is not a lot of space? Almost looks like the design for a duck house not a chicken house! would be a great spot for a pond.
3. I would definitely move the roost bar down a bit, and if you want to keep one higher, maybe have them going across the coop not running along the wall of the coop.
It looks well-constructed anyway!