What about mixing A and B whenever necessary? with B being the predominant one?
At first they looked like snowflakes to me, fat round and circular snowflakes, that were slowly falling, maybe with some snow scattered over the roof, and with some of the snow coming in-between the characters and the camera the effect could be more noticeable.
But then i noticed that some of those points are actually way too big for them to be snow, so maybe they really are moons or some kind of extremely big and close by planet, in which case... holly shit that's one hell of a planet! why are we dealing with ninjas and not with space pirates!!!!!?
VicariousE
I never thought you'd be using photographic terms, just shows how fucking tenacious you are :) I like B as well, and agree with your other assertions too... maybe if the clouds showed a bit of transparency when they're in front of the moon(s) and stars. Dim pics are okay, so long as finer details can be seen in the edges and BG... or is this an evening shoot, but with a couple polarizing filters over the lens (old trick to simulate night, but have even lighting)?