Thanks Markschum.  I looked at the geomstripper; I already have that functionality with D3D's poser tools program.  I couldn't find your python script, but I'm still looking.

I think I did find something to help me answer my question.  It kind of relates to the embedded geometry.  I opened a pz3 in Notepad++ and there were deltas for all the morphs.  This was even with the base V4.2.  It seems redundant to me to have those in the scene file.  It makes more sense to me to just store the morph channel setting, ie. "Shoulder Size = 1", and inject the deltas when the scene is loaded.  I guess that is where the pmd comes in, but wouldn't it make more sense to inject the deltas from the runtime instead of storing them with the scene?  I think that is where I am heading now that I have looked at it more closely.