The .cr2 contains the Judy-materials, the .obj adds the V3 materials and a single polygon of the 'iris' material from Judy. (V3 has separate materials for left and righteyes). This all together makes the material list a bit crowded and you lose oversight.

In my copy I have moved the 'iris' polygons to the left and right respective materials in the eyes (load the .obj in poser and re-assign the polys), then save the .obj (different name), throw away the .mtl.)

Then to fix the .cr2 open it in a CR2 editor (PhilC has one) or in a text edtor, remove all material definitions and fix the reference to the new .obj. Save the .cr2 with a new name and load it in Poser. If you then load it in Poser your figure will just have (a subset of) the V3 materials.

Loading an existing V3 MAT file will let you end up with all V3's body zones (SkinLeg, SkinFeet, and so on) in your figure. There is little you can do about that. In JudyV3 these are not assigned to polygons. All 'skin' is SkinTorso, or BodySkin for the alternate hip. The Genital material is specific for JudyV3. A template is attached.  

Judy always had an error in her original materials. Judy featured both a ToeNails material  actually assigned to Polygons and a Toenails material, an orphan in the .cr2. Case is important, in naming, so these are 2 different materials. This doublure of course disappears if you cut the materials from the .cr2.

For an EZSkin defintion for your new figure you can of course copy the V3 definition and select a shader for the genital material. In this elect forum I need not expand on the potential the special effects (wet, soapy) of EZSkin2 provide in this respect.