Just an addendum when I tried to create a new md5 with a more complicated rig and ran into problems. I was again getting that mesh stretching, and again, the fix was adding in a “root” bone that all other bones parent to, deleting stray vertex groups, and making sure control bones in Blender had “Deform” unchecked (although I don’t think that last part matters). I was able to do a reasonably complex rig and it’s loading ok. Now to animate and make sure that works as well.
Flow is Blender->AssimpView->Flash.