odf, for scaling, I think you may want to take a look at how DAZ did it in Victoria 4.  I think it may be easier than you think.  In fact, during the process of making the Beach Volleyball Set for Antonia, I have found that sometimes when I too concentrate on making thing to work, I ended up making it too complicated for me to finish.  I went through it already, crazy enough to make 3 JCMs for just one direction!  Now, the final version contains just 8 JCMs, half of them are mirrors.

I also found that I can modify the mesh without throwing away the JCMs for the old mesh, at least, it works in Blender.  I added and removed the vertices from the mesh created by the JCM as the same way I did it to the original mesh, the vertices order keep the same.