I can't believe there is anyone who has built them that doesn't think poop boards are the best thing since sliced bread. It takes me 5 minutes to scoop and shake the poop (my board is 6 feet long and 18" wide). Most of the poop is generated while the birds are roosting. If you spend that 5 minutes a day your coop and run will stay clean. I use pine chips on the coop floor they stay quite clean because I add to the chips weekly. I also use PDZ and DE on both poop boards and in the pine chips. There is next to no smell in the coop or the run. I also have a covered run. Anytime you add water to chickens you can have problems. Coccidia is always lurking in the coop. I will be adding an automatic waterer to my old coop and including it in the design for the coop I am building. I would beware of a wire floor the poop sticks to it instead of dropping through. Love your ideas. I will love to see your final product when it is built.
I second this. I have a poop board/tray with sweet PDZ under the inside roost and it takes seconds to scoop it out and I have NEVER had a smell, even when I left it for over a week (to see if there would be a smell).
We have a sand bottom run under our raised coop and that scoops/rakes out very easily as well. There's a link to my coop in my sig.