Am I missing something incredibly obvious here?
Yes, you have to select the model.^^
If that does not do the trick, you need to create a mmd model using the mmd_tools properties window (You´ll get that cross symbol at the grid center and a bone attached to it) and then attach the mesh to the mmd armature. You can also try selecting the armature and the mesh and convert it to an mmd model (apparently experimental). Never tried that though..