my only concern on this is that it'd get damp underneath the mostly-wooden structure. you've raised it to protect from rot, but have made it inaccessible to treat and check for termites. maybe it was sorted and the photos were never uploaded?
those nesting box holes might be a bit too close to the ground to hold much nesting material. you asked for advice on the boxes, but didn't provide good pics. some pics would be great.
Would like to see what you did with the recycled timber for the coop.
It looks like the run could do with some better stabilisers. Would love to see pics of the coop.
