Out of curiosity, would it be possible to use a 3rd uv set and scale it's uv to represent cloud shadows? Or would it work just as well to have a model of the level, with transparent cloud shadow map, and scale the uv of that model. ie the model would be independant of the shadow mapped one and slightly offset along the z axis? Or to get complex, could you possibly load up the cloud uv and write it over the lightmap uv by writing directly to the bmap, and scale it across dynamically?