Thanks for all of your suggestions! So we plan to knock out a bunch of the windows (probably keep some of them) to create ventilation, of course we'll cover up the new holes with something predator proof. We've decided to make a simple raised box like structure with nesting boxes enclosed so they have somewhere if they need someplace dark or if it's cold out. Of course we're adding a roof and some roosts. We plan to get the coop finished first and then began work on an adjacent run, we have a small grassy backyard they can free range in while we're there to supervise in the mean time.
I have some other questions but they are off topic so I'm going to post them in the appropriate sections.