I would get rid of all the bedding first and wash the coop out completely. What is your coop made of? If it's wood, mites supposedly breed in cracks and crevices. Heat in cracks and crevices should bring them out and kill them. I would use a blow dryer (of course you will have to have all bedding out before doing this) to see where the mites are hiding and the heat will also kill all life stages of the mite (eggs, nits, adults). Wear a mask or respirator if you do this. Wood is supposed to be warmer in the winter and cooler in the summer when compared with metal or plastic but unfortunately it is also better habitat for mites. Treat your chickens. According to Gail Damerow of "Chicken Health handbook" pyrethrum dust maybe helpful, baths are helpful. Petroleum oil painted on roosts, cracks and crevices can be helpful. You will likely have to repeat whatever you do for the chickens in 5 to 7 days. She also recommends you check your chickens at night when mites are more active. Apparently it will take some sustained effort to get rid of this. I haven't personally encountered this problem yet.
Also changing out the litter completely may bring on a fly problem next. But, I don't see an alternative. I think you have to completely clean out your coop and run, change the litter every week or 10 days 2 to 3 times until the mite problem is over.
Edited by joan1708 - 7/20/12 at 1:50pm