Reconfiguration successful!

I went into #1 with the plan to reconfigure.  My aesthetic sense was violated by the unusual set-up.  I expected the few brood I had last seen in the top box to have emerged and I could just remove the top box. Simple.
I brought over an empty box to hold the frames as I worked through them and put it on a work table.
The first few frames were either empty comb or a bit of honey.  Then there was some brood, honey and pollen and then, much to my surprise, I saw the queen, fat and golden.  I had been moving the frames into the empty box, but there was nothing under it.  I went back to the shed, dug around and retrieved a telescoping top that inverted and placed the empty box on.  Then I carefully moved the frame with the queen into the box, keeping my eye on her.  I selected four frames with brood, some resources and the queen to move into the bottom deep. 
After lifting off the medium, I went through the deep to find four frames to remove.  Two were easy to select- black comb, no honey or pollen.  For the other two, I found frames that were drone brood and larvae (I could tell by the size of the cells) and some nectar and pollen.  These would be sacrificed.

This is one of the frames.  You can see the scattered capped drone brood as well as some larvae (bright white in the upper-right quadrant).
I got the four frames into the bottom box, once again being very careful with the queen.  Voila!  A normal looking hive.
I scraped the old comb and sprayed B.T. onto the six I will keep and use again.  I looked at some of the capped drones and saw no mites.  Good news, but taken with a grain of salt as none of them were at the purple-eyed stage. This is when one usually finds the mites.