Winter here is crazy as well.. I have quite a lot of pupae being pulled out.. it gets warm, then it freezes, gets warm ,and then freezes... ugly situation...
if you have laying room down below, which i assume you do if you are seeing pupae like that being pulled out, then you should be just fine. As already said, they may have died in a cold snap and been removed.
Put the drawn combs in the middle of the second deep for the queen to lay in, don't worry about frames with only foundation unless you have a flow starting down there because they will not start drawing it yet, try to use comb if you have it. When the flow starts, pull the honey and give them some empty frames to draw to the outer edges of the brood nest.
Also.. you DO have mites, but you may not have many yet. We all have them unless we live in Australia.
I WISH I had the extra frames with honey.... Your in a good place right now!