@Reddog
Sounds like you are doing much more than working on the OBJ files, I'll be interested in seeing your scripts. Replicating the features of Poser file format is quite a hurdle. 
Since I use DAZ Studio and Carrara for my scenes and Studio's Skeleton Setup Tool to do all the rigging for conforming clothing, my target was to make Blender the modeling app necessary to do morph and new props. The only things that was missing was the ability to preserve and save the groups. My concern was also to integrate that feature in the stock importer/exporter of Blender so that there is only one source that is maintained from this point on. 
Now, regarding some of your observations about faces reduction and such, remember that for a morph to work it has to have exactly the same number of vertices in exactly the same order and the groups have to include the exact number of faces of the original geometry. But you probably know that already :)
Let us know when your CR2 exporter is ready.
 

Paolo

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