Let me start off with some information on what I do have... we live in Colorado so it is a dryer climate here. The shed has a window that is on the opposite side of the shed area. We don't have our run up yet so the chickens are being moved to a side yard during the day, and the ducks and geese are in a makeshift pen I made in the yard.
Our yard is separated into two sections, with a dog run area circling half of the main yard. The shed the coop is in is used as part of the barricade to the rest of the yard, along with a fence. The fence for the main yard is an ~6 foot wooden fence. Part of that fence blew down in a bad wind storm before we moved in. We were told the neighbors were going to fix it, but it is still not fixed. I don't know what the rest of their yard is like, what kind of fencing they have, or what if any animals they have. Currently with none of the flock using the coop by day, I've been keeping the main door open (it is directly across from the window) to help get a breeze passing through. However, once we get the run up I'm not sure how safe I will feel with that since part of the fence is down.
I used plyboard that was left behind from the previous owner to section off the coop area of the shed. We put in a door for easy human access, and but a "window" in the wall part of the plyboard to help with ventilation into the rest of the shed/where the window and main door are. Currently I have two vents cut on the coop side of the shed with open and closable vent covers (4x8) over them (they are on the same walls as the door and window, directly across from each other). The window is left open at night but the big door into the shed is closed and locked.
Obviously we need more ventilation, which is what I'm working on today. I want to make more holes for vent cover to go over once we have them (I currently have one more to put up) and since it's hot and summer time here I was going to cover them with hardware cloth until we get more covers. But my issues is knowing where to place them.
I took out a shelf that was built into the far side of the shed (one of the walls that is now the coop) but there is still a second shelf there up higher that we are going to keep. I'm sure it will be used for storing things such as bedding etc. should I put vents above the shelves, where they could potentially get blocked eventually, some just below the shelf (I can't do this all the way across because that's where their roost is and I don't want a draft on them at night), or both?
Another question I have is if the smaller door inside the shed into the coop area needs a wire mesh "window" like the wall part does. I hope all of this makes sense. I'm adding some pictures of what we started with, and what we currently have, so hopefully they make things more clear.