I have a seperate SHIII/GWX 2.1 setup for the S-Boat mod and only run this mod with it. One item though is that not all of the quick missions can be run with this mod as the S-Boat is a surface boat and most of the quick missions start under water.
If you have hard drive space you might want to start with a fresh SHIII & GWX 2.1 and then add in the S-Boat mod.
Hope you straighten out your problem and get this mod running. It's worth the hassle and a blast to have in the game!
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