I haven't read all the replies, but can you simply double the depth--garage in front, coop in back--essentially building a 4 car garage--2 wide by 2 deep? With a wall inbetween to separate the areas?
I have a friend who turned their extra garage into a coop. It is essentially a double depth garage as I described. She built pens along each outside wall of the back areas, then put in pet doors to let them out to a run that surrounds the back half of the building. The pen roof is partially covered with solid roof, completely covered with wire. She is out in the boonies, and has had to contend with bobcats, havelinas, skunks and raccoons.