I do not think you are being stupid. These are good questions. Your idea of a change in temperature being related to a change in the motion of the atoms, and the cause of the gaps that Hydrogen makes in the water molecules when freezing, is also very insightful. Although, it seems that it is not so much an instability as it is a locking in place.
Generally, I was thinking that since water is "thermodynamically backwards" from what is expected (both expands and decreases in density when cooled), it might be related to the fact that Hydrogen, which is the cause of this behavior, is predominately "generoactive" on Walter and Lao's periodic table.
But after a little more research it seems there is something else going on...
Other substances that expand on freezing are silicon, gallium, germanium, antimony, bismuth, plutonium and other compounds that form spacious crystal lattices with tetrahedral coordination.