The way my hurricane (v2, I am assuming that we are using the convention that Alfamike's is v1), works is that all the nodes doing the math combine to procedural mask having values roughly between zero and one. This is then used as the Blend Controller of a Merge Shader, which blends between a constant (Clear sky), zero and a standard cloud Density Fractal. When you apply the output of the math to the terrain as a displacement the areas with a value of one become highly displaced while the areas of zero or not displaced; exactly the same as if you used a grey scale image as the displacement function.
I don't think there is any way to procedurally lover areas of the base of a cloud layer so am fairly sure that neither version will be able to create the lower portions of a tornado. I have a couple of very vague ideas of how to do this but doubt I will get the time to try anytime soon.
I assume your initial image is of a v1 tornado below a v2 storm?