I'm a little late getting to this, I know, but I finally had time to peek in yesterday. I admit I did not do a thorough inspection because they were pretty testy and buzzing my veil by the end. Here's the findings and a question: The set up is one deep with 4 shallows on top. Top shallow was heavy on one side with mostly nectar and some capped honey. Full of bees. Shallow #2 was full. Did not dig into this one to see if it was brood or honey. Between Shallows 2 & 3 was burr comb with drone brood that I pulled apart. Shallow 3 mostly brood. Shallow #4 slightly lighter, but again I did not look into this one. All shallows 2-4 had at least 8 frames of bees The comb in the bottom deep is nearly empty, but there were about 4 frames of bees down there, and some patchy brood in the two frames I pulled. The SBB was littered with little white larvae carcasses - I suspect this weather caused chilled brood. Since the deep was not empty, I did not move or remove it. Cleaned off the SBB and restacked in same order. My question is this: Given that the bottom is nearly empty and the top nearly full, when do I want to put on a super? I would like to encourage them back down into the deep, but would prefer they did not swarm away.
The theory is if you leave them alone, they will backfill from the top down and force the queen into your deep. You say shallow # 2 is full, do you mean with bees, capped honey, brood, etc.? (Sorry, just reread that you did not dig into this one). If there is a lot of capped honey still in the hive and the bees haven't moved down, I might be inclined to super, till I had a chance to thoroughly go thru and rearrange things, just in case they get it in their heads to swarm.
If there are 10 frames of capped honey, I would harvest one super. Then I would find the queen and put the super she is in on top the deep.