Unusual configuration

This is the current configuration of #1.  This link discusses the common variations.  However, nowhere have I seen this set-up.  It did not come about by choice.  When I harvested the honey last fall there was still brood in the medium box so I left it.  I have checked many times and there has persistently been brood in the medium.  I left the bottom deep box in hopes that the queen and court would move into it.
Then I had my nuc.  I put the five frames into a deep box with follower boards to limit the space and put it in place of #3.  Well, as you faithful readers know, the colony lost its queen, so I used a newspaper combination in order to save the remaining bees.  I expected them to all move into the lower boxes and then I would take off the deep and have a single deep brood box.
So...
Yesterday I took a look into #1.  On previous inspections the bottom deep had only drawn comb and some honey and pollen.  If that had still been the case, I planned to do a lot of manipulation to get one deep brood box.  If the brood was gone from the medium, then I would rearrange to two deeps.
But the bees were not privy to my intentions.  There was brood in all three boxes!  I saw my (lovely) queen in the top deep box.  There was a fair amount of drone brood as well as worker in the bottom box.  What to do?  I added enough frames to make 10 in the top deep and left it as it was.
I did see a lot of uncapped drone brood and many with holes in the cap.

This picture is from another website and shows both uncapped larvae and caps with holes. 

I figured there must be a moderately high mite count.  Since I had intended to do a spring mite treatment anyway, I did not do a count but just put in Mite-away Quick strips.  I had to do some thinking about where to place them since the instructions say to place them between the two brood boxes; no suggestions for three boxes.  I did a bit of chemistry research and learned that formic acid fumes are heavier than air.  I put the strips between the medium and top super.  I also took out the entrance reducer to provide proper ventilation.

Olea's continues to go like gangbusters.  There were a total of 15 bars.  I saw brood on bar 14.  I added two more bars; 17 total now.

There continues to be sporadic activity around the swarm traps.