Well, I'm not specialized in making models, but I think the most accurate solution would be learning how to make & edit models. There are some tutorials of how to do it. Consistency problems could also be caused by imperfect model porting. For example, renaming Zoey models in the ".mdl" file to Bill can make the models available as Bill's skin mod, but as it's originally Zoey & it doesn't undergo proper porting method, the consistency problems could be triggered.

Probably you can also ask some people here who are specialized or good at making models by sending some private messages. You can check "Mods" section & list those who often make models. Who knows that probably some of them have the solutions you've been looking for.