Thank you for the responses. The door to the coop gets left wide open during the day and there are small holes in the walls. I actually don't have any pictures but I'll try to get some tomorrow. There is one window that opens at the top of the coop right in front of the roost that I have been leaving closed. I tried the deep litter method but it did not seem to work. This coop has wood floor with vinyl over it and a small layer of pine shavings. We refresh once a week, usually on Sunday. I'm not sure if I started out with enough pine shavings for the deep litter. I added shredded paper/cardboard as well as some dried leaves from around the pen. I mixed it once a week. Maybe I didn't spread out the collection of droppings under the roosts enough? Or water got in from rain. It started to smell really bad in both coops so ai just ended it and went back to changing it out each week. We don't really have a 'run' but just a fenced-in area surrounding the coop. We let them free range all day. I give them warm water every morning we have 3 1 gallon buckets for our 28 chickens. I live in West Tn. Right now I am feeding them a 22% protein feed with the scratch morning and evening, however I can switch to a 16% now that most of them are done melting and just feed scratch in the evenings. In regards to the hens I mentioned, the one in the photo has been acting normally from what I have seen. She is extremely skittish, even within the flock and waits for everyone else to get away from the food before she eats generally. Or she hangs around and waits because she generally will get pecked at. I try to make sure to give her a handful of food to eat separately about 30 minutes before it gets too dark to stay out. She is one of the last ones in at night so it's just the youngest 3, the rooster, and another hen or 2. The one with the bare back is actually the worst I have ever seen our hens. It is a huge area from the tail almost to the neck, I can get a picture tomorrow. It is completely bare and no new feathers have begun to grow in, or they have just gotten ripped right out. We have one rooster with that flock, but two from the other flock tend to go after the older hens. She slept alone so I hope she doesn't get cold. They have been packing themselves pretty tight on the highest roost. We have another roost about an inch down that a few use. The second coop is a large plastic shed. Two large front doors and two small side windows. I have been leaving the windows closed but opening both of the doors. There are 10 pullets(first ones just now starting to lay) and 3 roos. We tried the deep litter in there as well but water keeps getting in when it rains in the back and one of the sides. We have tried to cock up the bottom on the outside but we're going to have to figure out where it is coming in from. This was the first coop to fail the deep litter. It had an awful smell. I didn't really take care of this one as much or add nearly as much pine shavings as I should have as well so it was really expected. I just didn't want a ton of stuff to fall out as the doors were opened. The first coop has a ledge. So the floor is plastic and water gets into it when it rains. Other than that it is pretty great at blocking drafts. The windows technically lock but we have chicken fencing over them so not all the way but they stay closed for the most part.
Edit: I am going to check the hen with loud breathing for any discharge or cough tomorrow morning. Hopefully it's just from the cold air.