I'm just installing GWX on my Steam SHIII myself, so am no expert. I don't know how to uninstall the GWX mod, but I suspect that if you will delete the SHIII folder in your /steamapps/common folder (in Program Files/Steam or Program Files (86)/Steam), and then delete the other folders mentioned earlier in the thread, you can reinstall the Steam version by opening Steam and then right clicking on SHIII and selecting properties, click on the Local Files tab, and click the Verify Local Game Cache. This will redownload all the game files.
THEN, when you install GWX, you have to make sure you point the installer to the right folder. It will look for SHIII in the default Ubisoft folder, which you don't have. You just need to browse to your Steam SHIII folder and let it install there. That's what I did, and it worked for me. I can start the modded game with the GWX desktop icon.
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