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The method I used with the .ms3dascii export and so on is not a good way to do this any more, it is very error-prone and will not produce a good animating mesh because you will only have single vertex assignments and no morphing of the added group. It was good in it's day, when it was not possible to do this with any of the available tools, but that method is very much obsolete now.
I am also not sure if it will even work to add a third group to the mesh.
I only did it that way because the earlier BodyChop plug-ins couldn't handle extra mesh groups.
The UniMesh plugins fully support multiple mesh groups, just use them for all the editing and don't use the .ms3dascii import/export at all.
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The other problem, the "no quateration values" error, means that you have lost the comments of the bones - and also probably the group comments.
These comments are very important, and must be preserved or you will not be able to export the mesh.
That will happen if you export the mesh to an outside uv_mapping program, or to another 3d editor and then try to bring it back into MilkShape.
Never export an un-finished mesh as anything but a GMDC file if you plan to bring it back into MilkShape. You can also save it as a .ms3d file (DO NOT export as a .ms3dascii file, it is not the same thing!), and never edit that file in another editor - in other words do all your editing and uv_mapping in MilkShape.