I removed the top two medium boxes, above the inner cover, with the deep frames that had had some left-over nectar in them. I inspected those frames and it looked like virtually all of the nectar was gone. Plus, there were very few bees on those frames.
I looked into the medium box below the inner cover and it was jammed full of honey. So, I added a medium box with 8 new, undrawn, beeswax foundation frames. This is so that the bees could have some more room to put the additional left-over honey and nectar I was about to give them.
I set a 10-frame, deep box on the very top. (I have no 8-frame deep boxes.) I sat it above a 10-frame inner cover and taped the slot where the overhang was so that the bees could not go in and out there.
I put the three frames that I had harvested honey out of in the 10-frame deep box so that the bees could clean them up and take all of the left-over honey and nectar down into the hive.