I think it might take some thinking, but you could probably cut some squares out of it for ventilation. You might try using a circular saw to cut out the areas. Or a Dremel, which may work better. It's gotta be something that will actually cut through the material without catching the edges and cracking it. Or, if you can rig something up that will get hot, you may be able to melt through it. If you have the patience you could even try perforating the edges of the window. All it would take are about 2 million drill holes VERY close together around the perimeter of the window you're cutting out. LOL!! Oh, and a serrated edge steak knife to saw through the plastic in between the drill holes. One thing is for sure, you definately need ventilation. As far as windows go, instead of putting cardboard over the wire-covered window holes during the winter you could use a drill and some screws/bolts to attach a window frame to the outside of the building (by frame I mean any random pieces of wood that can be put together into a square) then put a piece of OSB or plywood on hinges and with a latch. Actually, if you drill some holes you wouldn't even need a frame, just some bolts. Bolt the hinges to the plastic, then use screws or more bolts to attach the piece of plywood (or whatever you're using for shutters) to the other half of the hinges. Then bolt a latch to the window and building. For extra insulation you could put some weatherstripping around the window shutter. Attaching the HARDWARE CLOTH (don't use chicken wire, predators can chew/tear right through it) should be easy. All you need are some holes drilled around the perimeter of the window and some HEAVY DUTY wire, or a coat hanger. Pass the wire through the holes and use it to secure the hardware cloth to the building. Make sure you're thorough and that you don't leave any spaces that a predator could nose through around the wire.
Anyways, post pics of your setup when you're done!!! Good luck!!!!