Sounds like the problem is with Destinations. I don't think there's anything I can do about that.

There are no QC files in Source 2. You should be able to fix the texture problems by making the right materials in the right location and then do a pure DMX import.

The Source Tools export each object relative to its own origin, not the scene's, unless it is parented to another object. If you need to align meshes with each other (e.g. Groups, collisions, gibs) then make sure that they are all parented. Create an Empty if need be; the parent itself doesn't have to be part of the export.

Please upload the files somewhere.

In the Mesh Properties tab you can name each vertex colour map you make.

I don't try to reconstruct sharp edges because doing so is inaccurate. There is no guarantee that Blender's auto-generated normals will match the input data, especially if the artist has done clever things like having non-unit normal magnitudes or "brushing" normals in a particular direction.

The polys are disconnected due to a limitation of Blender. As Zappy pointed out, when you run the merge doubles operator it will completely change the topology of the model and result in messed up normals (if you have custom normals) or edges (if you have reconstructed sharp edges). There's nothing I can realistically do about that. The answer is to use DMX, which does not suffer from this issue.

Vertex colours are supported in Source 2. You need to provide a specific name for the map though. Check the change log.

There are lots of extra things going on. I'm not sure what's happening in your case, but I've never heard of it when dealing with Studiomdl animations.

The Tools don't support the extended feature set of SFM animations. Sorry.

Make the scale of every axis the same, e.g. 1.5, 1.5, 1.5.

Is the error message not clear? You need to make the scale of your armature uniform.