That sounds good. I would not block any of those openings on the outside shed. Being that the coop is inside a shed, and well below those upper vents/openings, you should not have to worry about a draft on the chickens, But, a lot of stale air should be drawn out of the coop itself by those upper shed roof vents. In the Warmer months, you could have a hardware clothed "Screen" door as the entrance door, for the shed. That would allow even more fresh air for the summer months, but it would be secure from unwanted visiters. You can easily build the door with some 1X4"s and 1X6" pine lumber, sandwiching the hardware cloth in between boards. I built one for my coop. See the pic below.
Jack