Fukuoka mentioned that he raised chickens (even after the highway), but he didn't mention much about how he raised them. Did he use a coop? If so where was it located? I'm also wondering if the deepest soil that Fukuoka managed to build was where the chickens ranged, or elsewhere?

Let's see, Fukuoka-san's chickens...He raised chickens in the orchard which all together is about 10 acres. The chickens were allowed to range freely but generally stayed in the neighborhood of the huts. Among other things they pecked at insects in the posts that supported the huts and so extended their life span. In the evening the chickens were called in, fed a little bit, then put into a coop to protect them from animals. The feeding was just a little bit and was mainly given so the chickens would come when called at nightfall. So, yes, the chickens were raised in the food forest where the soil was deep and rich from the continuous mixed ground cover. In the early years Fukuoka-san raised ducks at his house in the village and brought them over to the rice fields during the day. They fertilized the soil and helped control weeds. Ten ducks peovide all the manure needed for a quarter acre. A highway was built between his house and the fields around 1960 which made it impossible to do that anymore. After that he spread a little chicken manure every few years instead which he got from a neighbor's coop.

Haha, he makes his chickens sound like they're magic or something, but that sounds like normal chickens to me. I think he underestimated good old Leghorns, everyone who's raised them says they're the only chicken that forages well enough to lay through the winter.