I'm going to guess that it was a pupae, since it is pretty difficult to figure out the difference between a drone larvae and a worker larvae. :roll:
And even if there aren't many mites spreading it directly, the Deformed wing virus is still hanging around in the hive. Could just be a few here and there that catch it.
Could be a SHB larvae that is burrowing below the surface. Or a wax moth doing the same. Chalkbrood mostly affects larvae, and you can identify that by what looks like peices of white and grey chalk laying on the bottom.
You are describing what is usually DWV. Don't worry about 1, the bees are pretty good at identifying the bad pupae and disposing of them.
Rick