Well, i don't want to hamper your enthusiasm, but i have a feeling that even a place like ILM would think twice about the sort of shot you describe!
Off the top of my head, I can only think of maybe 2 movies that have done hardcore thunderclouds/monsoon effects, and both were ILM; twister, and the perfect storm. Both involved some hardcore programming, and substantial modifications to off-the-shelf tools. The best commercial tool for sky and sea effects, arete, does littly fluffy clouds beautifully, but I've not heard of anyone using it for thunderclouds.
I just get the impression that you'll spend a lot of time fighting particle systems and sky plugins, and still not get anywhere near the result you want, whereas you could grab several cloud timelapse elements, either from stock libraries or shooting it yourself, and comp them together in flame/inferno/blah. Same goes for interaction with cloud elements, it'd be much easier for a flame operator to fudge those effects. Maybe even a cloud tank? Controllable, and easier to blend with 3d elements (just use green or black stand in physical models that you can replace with 3d), I believe most of the cool cloud elements in 'james and the giant peach' were done this way.
Pass it off to the 2d department, you'll be busy enough learning maya... 
-matt