Nope - I think @LisaMarie81 is telling you to remove the second story flooring and open up the entire house as one, tall unit. "Replace" the flooring with a couple of roosts. You'll need to leave enough flight room for them to fly up to the highest perches. They won't miss having the floor and they'll have more vertical space to move around.
Yup, that's what I meant. Treat the whole unit as one large box, instead of a large box with a tinier upstairs box. It's the quickest "fix" for a coop/run combo like that, to give it usable floor space and add ventilation/light all in one move.