Both of the things you said are because how the game developers intended the model to be.
The heels, I think it involves the skeleton of the model. In Skyrim for example we could see a lot of glitches caused by models that used the high heels, and others that don't, so I think the developers were wise enough to make it all look like they are wearing heels, and basically all of the shoes of the game have heels, so it doesn't make sense they change the skeleton just for that.
About the nipples, they are actually where the original model was intended to be. We could see nipple normal maps even without the mod, and they are exactly the same position where the nipples texture were added in this mod.
To make the nipple change place, we would have to edit the diffuse texture, normal maps and specular texture and probably have to remodel the original model, because I think even the geometry of the original model has the nipples in that place.
Anyway, the only way to make what you want possible, would involve exporting the model to a 3D editing tool, editing, and then re-importing, and no one knows how to do that for this game, unfortunately :/
