It's really best to do a full re-install and make sure nothing else is added before installing GWX.
End the stock career by going into port before applying the GWX files. Your grammophone directory should keep your existing files and will get whatever new ones GWX adds. Make sure that any mods you added to stock are disabled through JSGME before installing. It is possible that the textures you've added may cause a problem depending on what files were touched/added.
You can always use Multi-SHIII to let you run more than one install so if you want to keep the stock version you can HDD sapce permitting.
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