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The Blender plugin doesn't seem to export all the information that MilkShape does. In my experience, morphs don't "transfer" properly, either exploding or not importing. My workaround is to separate the morphs into different meshes (bake the shape keys), import that into MilkShape, and give them the morph comments there.
However, the round-trip isn't necessary unless you have waist seams to fix on your morphs. As you probably know, morphs are handled via shape keys. The morph and bone comments I think are added by the plugin. The transparency sorting information you can add in
SimPE instead.
Not sure about the "too many joints" error. I always import the skeleton as well as the mesh into Blender, maybe that fixes it?
(Btw,
Nopke updated the plugin to Blender 4+ here. I'm still on 3.6 too, though, so I don't know if it works for everything.)
I'm
http://crispsandkerosene.tumblr.com/ on tumblr, admittedly not very active on MTS.