List all needed bones in .qc using $definebone's. Those which aren't listed won't be included in compiled model.

You'll probably need to duplicate your old mesh and re-rig it on newer c_ skeleton. And re-animate it. The easiest way is to use constraints.

The Source Engine itself doesn't support bone scaling in animations. What exactly you're misunderstanding?

You might try using flex animation if you can figure it though...

So the problem is that vertex on the end is being still? Maybe you forgot to assign it to desired bone.

There is no anti-clipping mechanism for jiggles. You have to adjust jigglebones' angle limits to somehow avoid that.

Try exporting SMDs

Just select only reference mesh in object mode and expot it.

Rotate it?

Sometimes It's better to import just reference model instead of whole qc so it won't be messed up on scene. Some qc's might be very complicated to handle them properly.

The problem is that BST exports smd's with bone weighting. GoldSrc doesn't support this. That's why your "bones are not being exported", because studiomdl thinks these bones have no vertexes attached to them and cut them. The only ugly solution I found is to import your exported mesh into Milkshape3d and re-export it without bone weighting.

Animations should be exported fine AFAIK.