The things you are uncertain about are not mentioned in the milkshape ascii format. So i gues the only have purpose for the milkshape editor. Did you try filling them with zero's and see how the milkshape editor behaves when loading it. As brainer said when using the ms3d file you dont use those properties.

My gues on referencecount is about on in how many faces an vertex is used.
You may go for an group per material way. Alternative you may try to assemble a meaning like a leg or the head. Again i suggest you experiment with that. Again milkshape ascii only knows smoothing groups and does not use groups so they probeably are just convenient ways to quicky select some faces quickly.

I only have finished an milkshape ascii mesh exporter. But have not yet gotten around to export the skeleton with bones and animations yet.