That's a lot of questions for one thread.

I'll give quick answers and maybe you can try things out and post more in-depth questions in separate topics when you're ready.
For height variation, you can't control this by a shader or mask with a single population so what you would have to do is have 2 populations and control their relative distribution with masks so that they appear to blend 2 sizes of the same model. For your purpose, you'd probably use a Distribution Shader to control distribution by Altitude.
There are many parameters that affect the look of clouds. A hurricane or tornado is quite a specific thing though, it's not just "stormy" (for which you could increase density and coverage, and also darken the colors if you like). Creating a tornado is possible, but is probably a bit advanced for now. Fortunately you can get a pre-made tornado scene from NWDA to get you started easily:
http://www.store.nwdastore.com/atmospheres-cloudsAnimation can be imported using CHAN data (for camera), or FBX (camera, lighting). You can also use OBJ sequences, which is what you would need to have an actual animated object (as opposed to camera motion, or simple object "translation"). To get the camera into TG from Maya, use FBX or CHAN formats.
- Oshyan