It's hard to suggest fixes for "just messes up".

I don't think you can. Just make sure that you don't have multiple copies of the same armature from different sources. If you have the ref mesh and animations in different blend files, link or append the armature from the ref mesh one to ensure that it's the same everywhere.

The order depends on the order in which the bones appear within the Armature. Make sure that all your animations are on the same armature object and export them and everything should be the same.

If your animation applies to both of those models, yes.

You'll need to export the reference mesh as well as the animation when you change the bones like that.

Sounds like you're trying to import a Source Filmmaker animation. That isn't supported.

Make the scales match..?

It looks like your animations are being exported at a different scale from your reference mesh.

You need to parent your meshes to the armature. Anything without a parent will be exported at the origin.

Thanks for working that out xDShot! If you have a bit of scripting experience it's easy to fix up your SMDs for GoldSrc. You need to parse the triangles section and translate the weights at the end of the line into a bone ID at the start. Here's the spec.

I'll probably add support for this in the next release. Are there any other GoldSrc incompatibilites?