Do not install the game in the default Steam installation of "C:\Program Files (x86)", and do NOT install it in "C:\Users \UserName \Documents \SH4" or any other folder under "Documents". Both of those folders are heavily guarded by Microsoft Windows against any and all "un-authorized" changes. Anything "legacy", which would mean any DirectX v9 game, whether Silent Hunter or any other title, has the same "restrictions". This is not to say that the games are bad, or that JSGME is bad. The reason being that Windows will rollback any "system file" changes, which includes cfg, ini, exe, dll, and others, to their previous state. This results in a partial mod activation which can be worse than playing an unmodded version of the game, since the potential for crash is greatly increased.
If you have Steam, you HAVE to have a Steam Game Library folder that is NOT in a Windows protected folder. To accomplish this, you have to follow Steam's advice at
Moving a Steam Installation and Games in their Knowledge Base section. But if you have a 2nd viable hard drive, you can create a 2nd Steam Library folder on it, and install the game there. In all cases though, a player should install the game in a folder of their own creation, such as C:\Games\...". Steam itself will still be in the Programs Files folder system, but the game cannot be.
A person does have to empty any previous Save folder, which is found at "C:\Users \UserName \Documents \SH4", in order for the modded game itself to re-create when you start the game after applying the mod. The game, for the most part, runs off of data in the Save folder. A player can use
MultiSH4 to create a new 3-character named folder for their Saves...
If you do not follow instructions given with the mod in the first post in this thread, or on the download page, or in the pdf files in the mod's Support folder, you most likely will have a modded game plagued with CTD and all manner of frustration. This advice applies for ALL SH4 and SH3 mods, not just FotRSU.