Mason, being in Ga., you have somewhat of a flow going on. I would remove the medium, place the deep on the bottom board and the shallow on top of that. Using a sheet, large piece of plywood, or cardboard, I would slowly disassemble the medium right in front of the hive. The bees and the queen will march into the deep the same as a swarm will. If they are as loaded with mites as you say, I would sacrifice the brood and use the brood break for a mite treatment. If mites are not a problem, then salvage what brood comb you can and wire it into deep frames and put it in the bottom deep.
With so many SHB in your area, DO NOT use two empty deeps in the beginning.