Looking at the part of your CR2 that you published above and based on what you've said, I think it's a good bet that the PBMCC's are all empty channels and can safely be deleted.

Did you know that you can have Morph Cloth do the morph injections for you? Load basic V4 then hit the "Inject" button on the lower right side of the program window, a popup will allow you to select what Injection sets you want to install.

Binary Morphs are a gray area, you don't NEED them especially for this since you only have a few morphs in the shoes. For larger morphs it makes the CR2 file smaller and therefore load faster. Personally I like them and have had no problems using them, but others have reported problems with Binary Morphs and are leary of them. If you are making this as a commercial product I'd advise you to NOT use them and just save the shoes with the morphs imbedded.

I these are flip flops why make them conformers at all? Simply parent them to the figure's toe group, this will make them a little more realistic since the flip flops will move with the toe and not bend to stay attached to the foot group. Doing it this way tho may mean making a Joint Controlled Morph for the straps for extreme bends depending on how they are modelled.