Well you've got the cleaning sorted, maybe a bit much though how often you clean the coop is a personal thing. Can you get hold of jays fluid? flies and maggots hate it and the smell ( humans also) a bit of that diluted in the house/ round the doors should help. otherwise hospital grade detol diluted works well, put it in a pressure sprayer and after cleaning out the bedding give the entire house a spray, leave the door open so that it can air out for a bit. Have you considered a fly trap/ those sticky fly things out of reach of the hens?