That is probably part of the problem. Way too much space for a package. One box is plenty. They will be spending a lot of extra energy trying to heat the second box. I would take the bottom box away if they aren't using it.
A decent queen can easily lay 2,000 eggs per day. A langstroth frame has 3,500 cells per side. So she can half fill one side of a frame in a day. However, her laying will be determined by space, heat and stores. If the bees haven't drawn much comb, she can't lay that much. If the bees can't keep the space warm, she can't lay much. If they don't have many stores of honey and pollen, she can't lay much because they don't have anything to feed the larvae.
A healthy hive will have brood boxes with approximately 60% brood, 20% honey and 20% pollen, according to my mentor. If that is about what you are seeing, the queen either doesn't have enough drawn comb yet, or they don't have enough supplies to support more brood.
That will certainly slow them down. Plus they will be eating the stores to keep that enormous space warm.
You probably did them a big favor by reducing the entrance. They would find it easier to keep heat in the hive. If they have only drawn 2 frames, and the weather has been bad, I would keep feeding them, and keep the entrance reduced to between no more than 1/4 and 1/2 of the full width.