You need to get a necroscopy done on one of your deceased chickens STAT. Disease can wipe out entire flocks in a very short time and put other nearby flocks at risk. I'm so sorry for your birds :( if you google "the chicken chick" blog she has some links to free services to quickly determine...
I was thinking the same thing about the ventilation. My hens preferred to roost outside last summer and I had to catch them and put them in their coop each night to protect them (that was before I made this huge enclosure). I was thinking more of an open format would be better than a closed-in...