JSGME is an application that helps with replacing files altered by mods:
http://www.users.on.net/~jscones/sof...cts-jsgme.html
It is automatically installed into the Sh3 gamefolder with GWX. But since you don't have it you must do it yourself. The application must be placed into the sh3 game folder, and it must be started once to create the MODS folder there. After closing the application you can extract the particular mod there in the MODS folder. When you start the application again you can enable the mod which actually replaces the files of Sh3.