Pasting some notes into an article for easy linking.
Here's my theory on the 'stack up' aspect to coop design, and a couple other dimensions and ideas:
Bottom of pop door is best about 8" above floor so bedding doesn't get dragged out of coop.
(If you plan on using truly 'deep' litter, might have to adjust this height.)
Nice to have bottom of nests about 18" above bedding to allow use of that floor space under them(doesn't count if your nests are mounted on outside of coop).
Roosts are best about 12" higher than nests so birds won't roost(sleep) in nests and poop in them.
Roosts minimum of 12" away from wall. Poop boards under roosts will also 'stretch' your floor space and can protect feeders and waterers....and are a unique way to manage manure.
Keep in mind that floor space is needed for birds to have landing room to get down from roosts/nests without crashing into something.
Upper venting works best as high as possible above roosts so no strong drafts hit roosts in winter...and hot/moist air and ammonia can rise and exit coop.
And Go Big ...3 separate sections for Main flock, Growout/broody/isolation/hospital, and Feed/supply storage has made my chicken life much easier. Actually wish I had made grow-out area larger(for ease of tending) and had 1 or 2 more sections.
Also.... Read this on how much Space chickens need....
and this on Ventilation