Just another observation/comment, re: Vert->NearVert correlation...

Keep in mind that since this method doesn't pay any attention to surface orientation/Normal,  a vertex on the inside of a nostril (for example) might well include (get correlated to) vertices on the outside of the nostril on the other mesh... the same thing could happen around the ear folds, etc. - basically any thin piece of skin-fold like that (eye-lids, lips, etc).
 
With the Nostrils, you can handle that situation easily enough with Material Screening (at least on meshes that have a separate Nostril material), but you might need some other method for things like the ears. 

A fix for this might be to do an angle check (between the two normals) before including vertices in the correlation and skipping them if the angle is too divergent (like maybe anything over 90deg).

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