Wow!  The template looks great!  It would have taken me forever to organize my thoughts enough to even create a template form for this.  :-P  I'm not very good at explaining myself to others.  I'll try to do my best, though.  Thank you for helping with the help.

Regarding the questions.  

1)  The script will automatically zero all morphs where appropriate for morph/shape transfer and the "extra" functions and will generally reset them after the run.  For the actual correlation process, when comparing the geometries, you may need to zero all morphs or selectively set some or create magnet deformations - whatever is required to get the best "match" between the two actors in the 3D view.  This will really vary on a case-by-case basis, depending on the actor meshes.  Mesh comparisons really are the hard part of this process, on the user's end.  And when transferring a shape, you actually want to have the desired morph set in the source in order to transfer it.

2)  I've had no experience with .chm files and Python, but I'll see what I can find out.  I would assume that it should be able to work.  As far as Macs are concerned, however, I hesitate to even speculate.  At this point, the script itself is not compatible with Poser Python for the Mac, because of problems with Tkinter.  So in the short term, at least, this doesn't seem like it needs to be an issue.  Again, I'll see what I can find out abouot this. 

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Cage can be an opinionated jerk who posts without thinking.  He apologizes for this.  He's honestly not trying to be a turkeyhead.

Cage had some freebies, compatible with Poser 11 and below.  His Python scripts were saved at archive.org, along with the rest of the Morphography site, where they were hosted.