You will need a whooooole lotta ventilation, if it's anything like the shipping containers I've known being used for hay/bedding storage or as (really not good at all) horse shelters. Like, a WHOOOOLLLLE BIG LOT of ventilation. Get out the drill and Sawzall. Seriously. At the very least (it's not sufficient, but it would be helpful and possibly necessary) don't run the pens too close to the open end of the container, so you can leave the end permanently open. That plus a buncha 'window' type vents might be sort of sufficient.
Second, if this container is not insulated then you are eventually going to need insulation on the ceiling and possibly walls too, because in the North you will get major condensation problems with nekkid metal walls like that.
Shipping containers really aren't great for housing livestock (or hay either, come to that)... you can *do* it, but IME not usually very gracefully.
Good luck, have fun,
Pat