I clean my coop once a week. I do have a new coop built and I am in the process of building a new run that will be sand. Where there pen is now is a mud whole doesn't dry out well ect. I have only had one sick bird we thought it was bumble foot but I am not sure it spread up her leg we culled because she was in pain and it was staph but that was our choice. The other birds I lost were to my son''s puppy. I do worm my chickens once a year but that it. I give mine a game bird feed 22% protein because they do free range and get grass clippings veggie scrapes, Boss, scratch I also crush up egg shells and throw those in their pen once a week or so I have really strong egg shells. If I was the OP I would cull and start over it just sounds like there might be some unknown illness I would also look at where the run is if there is a problem with mud and mold You might have to move the run or put down sand. When I clean my coop I put down straw and some DE the chickens usually stir it up for me. Good luck and I hope the OP can figure out what is wrong, Chickens should be a fun hobby not this much pain.