I'm assuming here that you are running Windows XP and NOT Vista. All the below applies to XP. If you are running Vista, you will need to back up your mods, uninstall the game and reinstall it somewhere besides the "Program Files" folder (for instance in C:\Games or on another hard drive if you have one available. Vista does some wierd things when you try to change files in the Program Files folder and is not really conducive to modded games.
No, it looks like you have it installed correctly. Just to double check, you could check the hidden folder !BACKUP in the MODS folder and make sure that the files in Sober's mod have indeed been installed. If the files have been installed, you will see a file/folder structure similar to the mods structure except the files would all end with the name of the mod (signifying that the file is the file that was in the game before the mod was activated).
The MODS folder should have been created correctly in the root folder of SH4 when you first ran JSGME and it should stay there. Moving it into the Data folder will not accomplish anything (except maybe foul the game up).
Maybe a screenshot of what's in each of the following folders might help us determine what the problem is.
......Silent Hunter
......\MODS
.......\MODS\Sober's mod
........\MODS\Sober's mod\Data
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