The first post of this thread has quite a few "Spoiler" tags with activation instructions, and the Support folder of the mod has pdf "help" files Silent_Theory. First of all, you cannot have the game installed under any of the Program Files folders, which is what Steam will default to. If the path to your game is "C:\Program Files (x86) \Steam \SteamApss \Common \Wolves of the Pacific..." or similar, then you will have to either un-install and then re-install the game in a folder of your own creation, or manually move the install. For more on that see
Moving a Steam Installation and Games from the Steam Knowledge Base. If you have a 2nd viable hard drive in your computer, you can create a 2nd Steam Library folder there and install SH4 in that new Library. There is a way to "fool" Steam into a 2nd Library on the C: drive, but I cannot find the thread just yet. In any case, the 'modern' Windows will prevent your updating of any file set in the Program Files folders, in an effort to protect you from yourself. Windows does not recognize the Silent Hunter games as proper Windows apps - written during for Windows XP during the "wild west" days of minimal OS "security" - and Windows especially does not like JSGME.exe going behind its back without proper authority and changing cfg and other "system" files. When Windows sees that, it does roll certain of the files back to their original state, and you get a mish-mash of the Stock game and the FotRSU (or any other) mod, which can result in error messages and then game crashes.
Secondly, be certain you are using the correct Steam SH4 start-up. It sounds like you might be using the Wolves of the Pacific startup, and not the U-Boat Missions Add-On version. If you use the Wolves start-up, you are using the Steam v1.3 of the game (they claim it is "fully updated", insinuating it is v1.4, but it is not). That is the usual originator of error messages of files missing, and if you get one about black80.tga file.
You have to empty the Save folder ("C:\Users \UserName \Documents \SH4") before you play the modded game, and you most likely have to set Properties on the SH4.exe file for Attributes and Compatibility, so that you can get a 4 gig patch file to enable on the SH4.exe file, and to tell Windows to leave it alone as it runs. The Compatibility settings are system dependent.