It's hard for me to figure set up with out seeing the materials and dragging them around, but i am a world class jerry rigger (self proclaimed lol) so we'll see.
First of all, i would place them on their wide sides, they are more stable and requires less wood. Plus, they're more out of the wind and you can pile straw etc on top and sides for insulation. If you can remove the bottom bunk's interior platform, ( not the bunk itself, you need that for stability), whether it's that fence type stuff or slats, I would do so.
Basically, you're building a box around the frame, I'd leave part of one side , the entry hole, (I'd use a long one) and the floor un-covered. Or you could make a low floor some how.
You can make some some nest boxes near along the back and some sort of door for access to them. You can cover the other bed frame in chicken wire and use as a run. If you're planning on using both as a house, then I would still remove the bottom bunks' wire etc and stack them and enclose. It really depends on your preference. Also, you can find cheap outdoor paint at thrift store or if you have a habitat for humanity restore, the usually have an agreement with a paint shop and can have paint pretty cheap, you can also wrap the whole thing in plastic sheeting for a wind barrier and water proofing. As for attaching the wood to metal, since I'm not sure on the frame's thickness, I'd use corner braces to attach wood to wood. The great thing about having a low Coop, is the snow acts as as insulation. I'll try to draw up a better example
edit for correcting the autocorrect