I like opa's suggestion, it sounds like the most practical way to go if you want plastic on your inside walls.
If you substitute ss washers for the neoprene gasketed screws, put a good blob of silicone caulk in the assembly before screwing it tight, otherwise water will leak in and start rot. (Which is of course why the roofing screws have the neoprene washers in the first place, to avoid that <g>). You can wipe off any protruding caulk while it's still wet.
FWIW I don't know what climate you are in, Rose Acres Farm, but if it's somewhere that gets down to freezing or lower in the wintertime, I STRONGLY STRONGLY suggest not relying entirely on the windows for ventilation, but making a bunch of dedicated ventilation openings high on all the walls (with flaps or sliders to cover when unwanted). If you try to ventilate the building using just the windows, in cold winter conditions, you will have real problems with cold drafts on birds.
For the ceiling vent, if you are talking about one of the turbine-style ones powered by the wind, make sure you have a way to close off the opening, as you will sometimes want to. If you are talking about a powered vent e.g. attic or bathroom fan, remember these are not designed to operate in super high dust environments like a coop and are really not such a great idea. You will spend all your time cleaning or replacing it as dust gums up the work, and they are a bit of a fire hazard. Also really unnecessary, as well-designed *passive* ventilation is quite adequate for virtually all noncommercial coops.
JMHO, have fun,
Pat