My barn started life as a cow barn, it's seen several changes in livestock types since then (we've had it about 40 years). One thing I've learned is to keep it flexible in arrangement. From ponies to goats to Dexter cattle and a mix of all together, and now my beef steer, a mini, chickens, and goats. I've managed to keep the space flexible according to my shelter needs. It's only about 40x30ft, with a hayloft above. I keep one large pen that opens onto the barnyard and gate to pastures. I would suggest you keep one large pen that can be partitioned into 2 when needed. As for size for minis, I'd measure your largest from nose to tail, then double it for minimum length and width of the box, trippling it if you have the space. It's also good to be able to lock your grain away from prying noses, even if it's just a wooden box to hold a couple garbage cans, that you can tie the lids down, and not get tipped over. You'll probably think of more stuff to consider in your re-model.