Wow, that's a beautiful piece of craftmanship! Soooo much better than their old one!
Are the boys littertrained? Are they chewers? Maybe you could line the floor with a fleece blanket (my boys love that) for now. You'll need straw in winter though to keep them warm.
What's happening with the run now? Are you going to make a cover for it? It'd be lovely if they could freerange all day.