What you have suggested is totally feasible! However, the pupae wouldn't have fallen from the roof above. Instead the maggots would have crawled around looking for a suitable place for pupation. In the out-of-doors maggots will often dig into soil and bury themselves, so it doesn't surprise me that they buried themselves in the fur of your daughter's toys.
To make a positive ID on your particular flies however, we would need a sample of one of the pupa. Even if you had a picture and a measurement of length that might work too. A lot of fly pupae look very similar. Common house fly, Musca domestica, pupa look very similar! (http://entnemdept.ufl.edu/creatures/urban/flies/house_fly01.htm)Lila