That sounds like far, far too little ventilation -- which would be one of the reasons that the deep bedding didn't work. If you don't have adequate airflow the bedding can't stay dry.
The respiratory problem could also be caused by poor ventilation -- chickens have very delicate respirator...
Where, in general, are you? Climate matters and we can give better-targeted advice if you put your location into your profile.
Don't overdo the treats. They need the solid nutrition of their balanced feed for good health, especially if anyone is molting and growing new feathers.
Also, don't...