A good rule of thumb is to try to build at least one square foot of ventilation for each chicken that will be using the coop. In order to be able to keep those vents open even in cold weather, put them up at the top of walls, ideally on opposite walls so you can get some cross ventilation. Flaps over the vents are nice so you can adjust them on the coldest nights, too.
Oh, and about the hardware cloth covering windows: you can certainly put the hardware cloth on the inside of the window if you fasten it securely. I use screws with large heads over washers bigger than the size of the openings in my wire. The wood on the window frame will give way before those fasteners do, and I don't think the wood is going to give way any time soon because it's 2' by 4' studs!