Nothing wrong with building a new wooden coop inside a wire run. I'd make sure the roof & sides of the new coop aren't too close to the wire of the run. If a chicken panics & freezes when a predator gets near the wire it could get hurt through the wire. If you doubt your carpentry-from-scratch skills you could purchase a shed kit or coop kit that is delivered in pieces. I've even seen them on Amazon.com. If the coop is inside the run it wouldn't need to be "as" predator proof as the one outside the run, but should be free from drafts & rain proof. I'm not as sold on the dirt floor thing. It would be easier to clean, IMHO, to have a solid floor. You can then put sand, pine shavings or Sweet PDZ on it, and scrape it out with a hoe when it gets soiled. That would also keep the birds from tunneling under the sides. You would only need a roof slant of 4" - 6" or so, from one side to the other, to keep rain running off, but the more slant the less easy for the birds to sit on the roof and poop on it. Eave length is not that critical. 12" works on most homes to keep driving rain off the windows. I would think a coop could get away with half that since there are fewer windows. Depends on what you want them for. You can make the coop as high as you want. If some of your birds can jump or fly well, height is no obstacle to you putting multiple level roosting bars in there, just not on top of each other (they'll poop on the birds below). To me, it's more important for the humans to have comfortable access to all areas of the coop & run. Your pigeon-toed girl is gonna sleep wherever she wants to, whether you have a designated place for her or not. Maybe if you put a covered box in the corner she'll go in there. They like to feel protected and not out in the open. Good luck!