What a beautiful coop! I kind of have a similar set up where I have my coop and totally enclosed run, then a much larger area done with chicken wire for my girls to roam! One question (I've never been a great reader) - Is there a base to your run, or is the hardware cloth apron the main thing to keep digging predators out? My apologies if I missed it in your fantastic write up 
I don't believe in putting anything but the earth and organic litter under a chicken's feet in a run. They need to be able to dig holes for dust bathing and scratch around in the run to look for critters. They also like to dig along the perimeter of the run in the damp soil when it's hot out and lay on the damp earth to help keep cool.