I've been trying to think of why bones and clouds might somehow be linked. The two things that come to my mind (though it might be different for others) is that in general I think we mostly think of clouds and bones as being similar in color (white). Although, clouds are not always white in appearance (the could be grey during a storm, or pink during a sunset).... still, the general notion is probably to think of clouds as white. And, both clouds and bones give structure (either visual structure or physical structure) to things that would otherwise be loose, amophous, unstructured, etc.
And, when it comes to the demonic energy of a mountain... I can think of ways that a mountain (its massiveness, dangerous craggy materials, etc.) could be thought of as threatening. There are ways that mountains can be beautiful and peaceful, and other ways that they can be dangerous (for instance, getting lost, getting stuck in a storm, feeling tiny in the presence of massive natural structures, etc.). I think the way a mountain can be perceived may be somewhat tied to personal mood at a given time... so that makes sense for the coming down the mountain mood in BBM.
Ennis's perception of the mountain as hostile all of a sudden (when it once was benevolent) is his internal projection.