I feel your pain. I had terrible flies last summer. I have a new coop with a covered sand run and am hoping it stays drier = less flies. So far, so good, we've had some warm days here in Northern CA and I haven't seen any, but the real test will be this summer. If they come back, my plan is to try the following:
-fly traps - the kind in a plastic container with attractant inside, the flies crawl in but can't get out. I've used them before, they get full of flies in no time, then you dump them out and add new attractant. It is gross to look at the thing full of dead flies, but I like that it is not toxic, doesn't smell if I change it out every 2 weeks or so (the only smell comes if you let the dead flies sit too long...I know, gross).
-DE and stall dry to keep everything dry, keep things as clean as possible (already doing this)
-fly predators - haven't tried them yet, but definitely will if the flies come back. I've read positive things on BYC about them. They are beneficial insects you can order online that eat flies, I think when they are in the larva stage
http://www.spalding-labs.com/
I think the fly strips help also, but my coop/run is so small that I end up bumping into it all the time...ewww!