Your AV trashed your install, along with doing what Windows does to a game when it is in a "Program Files" folder. So between the AV and Windows, you are being thrashed into submission. You will have to move your game install out of the "Program Files" folder. Consult that Steam Knowledgebase Article "
Moving a Steam Installation and Games". It is a major bother, and will take a while to accomplish. Activating the mod will get you one play - maybe - of the game, but while you are playing it, in the background, Windows is changing all of the cfg and other recognized file extensioned files back to what they were on the initial install. Since JSGME did the activation, a lot of the files are "invisible" inside of its database, so now you can't use JSGME to properly restore you to a good stock game state, which is why there were so many missing files when you did the Steam "check". Doing a Steam "check" on an install with an activated mod will essentially wipe-out the mod also, since Steam puts everything back to stock.
I don't know how many Steam games you have, but if all you have is the SH4, or maybe the Silent Hunter 3, 4 & 5 series, I would be tempted to do an un-install of the Steam app and the games, then re-install Steam, but during the installation, choose a Library folder location outside of Windows' influence, such as "C:\Games\" or whatever you want to name it. You do NOT want to put Steam nor the Library folder directly into the root of the drive, since that again is "system" territory and will be altered back, but also because of the potential mess you could possibly make of the computer if you did that. You will still find most the Steam app itself still in a "C:\Program Files (x86)\Steam..." folder, but your Library will be in "C:\Games \Steam \SteamApps \common \GameName" now, out of the direct clutches of all things MS and AV...
