Many thanks for the bullet point list Cage,  I'll study that carefully. No worries on the flowchart.

---------------------------------------  the following is not related to morph transfer script ------------

Oh the shorts are not forgotten. I have been trying to work out why it is proving so difficult for me to create useable JCMs for them.  I looked at the shorts you made based on Antonia's topology, which seem to work fine with one JCM. 
I hacked Antonia 122 CR2 to make the hip2 and thigh morphs independant from the thigh bends. If I apply the spread morph with Antonia joints zeroed there is some very sharp deformation of Antonia's mesh around the backside at spread -60. These obviously work well for Antonia, but I think the  approximation which is happening with 'morphing clothes' trying to replicate  the sharp deformation of Antonias mesh for 'spread', into the quite different topology of the my shorts is resulting in a morph which doesn't really do what is required of it.

My experiments were interupted with a three day ITIL course and exam, so I had to put 3D out of my mind for a few days. ( my old brain doesn't multitask as well as it used too ).

-------------------- we return you to your regular discussion about morph transfer script   :-) ---------------

Cheers

Ian