UPDATE:
So it's been almost 3 weeks since I moved the chicks into their new coop, they are now almost 8 weeks old and still growing like crazy. I'm noticing their "faces" getting redder and their combs growing out. They all have beautiful coats of feathers.
The coop design appears to be successful. The chicks easily navigate the space, use the interior ramp to get to the roosting area and get themselves on and off their roost. They also stay out of the nest boxes for now which is nice. We've just had several days of steady rain and nightly temps down into the 30's but the coop remains dry and the chicks don't seem to be bothered by the cold. I have a webcam installed so I can watch them at night and they huddle together on one end of the roost and puff themselves up and sleep.
The automatic pop door is working like a charm. It reliably opens every morning and closes every evening and the chicks have all figured out to go inside before sunset, get a bite to eat and settle onto the roost (usually with a fair bit of pushing and shoving) before the door closes and the interior light turns off.
Cleaning the coop has been no problem. Every couple of days I take out the poop trays under the roost, dump the shavings into the compost bin, hose off the tray if it needs it, let dry and reinstall with new shavings. It takes 5 minutes. The lower portion of the coop doesn't have much poop even after 3 weeks. I'm using the deep litter method for now, but the shavings look brand new so I haven't added any fresh shavings down there yet. I just stir them occasionally.
The interior ramp gets messier than I imagined it would so I am hosing that down every day or two. Why can't chicken go up and down without stopping to poop midway? Why do all the other then insist on walking through it? Their poop really sticks to the painted ramp so I'm looking for an easier to clean surface for that. I may cover it in the same rubberized carpet runner material I am using elsewhere. Nothing seems to stick to it, poop just falls off their roost without me having to scrape it.
The sand in the run is working out great. Even after all the rain, the run was free of any puddles and I haven't noticed any smell at all.
So all in all I am happy with the design so far. It is working well for my small space.