OK, I got very distracted last night just trying to get close to where you are.... Let's just say that I now have a far greater appreciation of what you have achieved so far
That left my morning train ride to refocus, and unfortunately I forgot to save often
Nevertheless I did manage to split up the image map into it's white and non-white components so that we can start to tinker with the border of the image map without affecting the rest of it. I'm not entirely convinced that this is going to be a big fix, and will probably be only useful in situations like yours where your clouds are fairly close to being what you want.
The biggest problem with masking clouds is the thickness of the cloud at the edge of the mask. If it's almost full thickness then you have a very odd looking cloud. The only way around this might be to break up the border with another fractal of smaller scale but this will still be of limited use... If however you're relatively close to having the right result then the additional border breakup may provide a subtle improvement that makes just a bit more believable...
I'll attach this morning's work although all it does is isolate the different parts of the image map. The zip file contains my test image so you probably don't need it. I'll persist with this test regardless of how well it progresses with clouds because it will be useful to me for my river masks
[edit] It would be really nice if there was an additional input in the cloud node that scaled the cloud thickness based on a value from another node. That would open up a lot of possibilities for creating different cloud formations without trying to mask the cloud fractal. Easy to say... possibly not that easy to program
[/edit]