What about Trying Drumming them up into the new hive body?  Drumming is a very old technique, mentioned in the very earliest beekeeping txts as a method of moving bees out of their old skep, and into a new one so youcan rob the honey from the old one.  The old skep was placed upside down, with the basket opening facing upwards, the new skep was placed over the old one, and then the beekeeper rythmacally and slowly tapped the old hive.  the steady rhythmic thumping is supposed to make the bees walk upward into the new accomodations.
I have also read a few modern accounts of beekeepers driving bees up out of log hives and into modern equipment using this technique.
It might be worth a shot-  drum them up into the new equipment, place a queen exclder below once you think the queen is up top, and then give plenty of space up top to set up housekeeping.  I agree that drawn comb, and maybe a frame or two of brood is far better than undrawn foundation.
If anyone has expereince with drumming- I'd love to hear about how it works!

If you are up for a big messy project, you could always take apart the doghouse, cut out the brood, tie it in frames with string, and force the issue- kind of like moving a colony from a tree or house.  (What a mess!  The pictures I have seen......)
Good Luck!
Ellen, in Michigan