Big swarm, big mess, need advice

I picked up a swarm yesterday that had actually moved into some old hive bodies laying around. The lady that called thought it was neat for the first month to have them flying around until the amount of bees in the air starting freaking her out, now she wants them gone. So I'm thinking here are two deep hive bodies with a tele cover, this will be easy, (go ahead and start laughing, I should have known better). So I pop the top off and this thing is packed with bees. The top deep only has five frames, but it's covered in bees and brood, the bottom deep has ten frames and is just slammed with bees. The five frames in the top deep are in the middle, but from the tele cover all the way to the bottom deep is natural wavy comb of honey. On the other side is wavy brood comb packed with bees from the side wall to frames in the middle. So I take this off and put a screen on the top and bottom to get to the second deep to find it's sitting a inch deep in mud. I put a screen over it and pulled it out of the mud and then combined them back for the ride home. Need suggestions on what to do next. The hive bodies are rotten and have entrances in multiple places so these boxes need replacing. The frames in the bottom deep will not move without destroying them so my first thought is to put a new deep on top and wait for them to move up and take the bottom away in later winter, but what to do with the second deep full of wavy natural comb and the five frames in the middle that won't budge either, perhaps get a queen and add a box on top and let them move up as well? I have very little drawn comb available right now so if I do this I have to do quick so they have time to drawn out the new foundation. This is my plan, any Thoughts on a different way to get them out of the rotten boxes and into and sturdy boxes where I can actually move the frames around? Thanks