Clustering 3D multivariate data
It would be nice show a few example data points to make sure that my answer is what you may be looking for, but anyways,

1) I think so, you may wanna look at feature weighting for k-means in this paper

3) For the libraries commonly used for this, you may wanna look at this answer or this code

2) I'm unclear what you mean here, maybe you could elaborate, or probably someone's going to pick up on it and answer you on this point.