I ended up extracting two deeps and a medium because the queen was in the top three mediums with no brood below her.. Worked out fine for me, and apparently her.
This only verifies the wisdom of my choice to use all medium boxes. I have both 8 and 10 frame but all mediums except for one deep that is not yet in use.
I can re-arrange frames without difficulties. Although I am still confused over just how much space they need for their own use before additional boxes can be considered "honey supers".
Some sources say the equivalent of 2 deeps, others say equal to 2 deeps and a medium, and there are those that are adamant that hives must be 3 full size deeps or more before any harvest.