I too would suggest that the one nest box come up off the floor. Three reasons. One, stooping to get the eggs is no fun, two, I found that when they are on the ground like that the hens will scratch in the litter and push the dirty stuff into the nest boxes, three, they will tend to scratch in the nest boxes and this can led to egg breakage and egg eating.
You can take the one nest box and place it over the other, your hens should be able to access it, it doesn't look like from the photos it would be too high.
The roost also concern me. I think you are going to have hens pooping on the hens roosting on the lower boards. As you know hens establish a pecking order and several will be pushed to the lower boards.
Again, great job in building and designing the coop you will have very happy and healthy birds.