Make a version of your CR2 with no JCMs to be certain it isn't those, and set up some kind of reference prop that is not rigged, so it won't be deformed in any way.  In your modeler make some kind of geometry that you are absolutely sure is 100% symmetrical, something with minimum poly count and simple (a pair of boxes maybe).  Place the reference prop on both sides of the figure and check the joints and see if the deformation really is symmetrical, it's hard to be sure just eyeballing it.

The asymmetrical falloff zone orientation problem can be seen in Poser (this doesn't happen in DAZ|Studio as far as I know) in any humanoid figure I've looked at, although it manifests in different places.  I don't know if this is the same as what you're seeing since you've adjusted the rig and fixed the X orientation of the center line bones though.

As to Morphing Clothes, after thinking about it some more, I think it actually will be simpler to use two reference CR2s to take the JCMs from, with one direction of bend for each - rather than pick through the clothing CR2 to try to decide which JCM is the correct one, just do it in two passes and remove any decision making.

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