X-Files main theme uninstall
To uninstall the X-Files main theme, that begins at the intro of the game, go to your Data folder at: Data/Video/MainMenuLoop/ and remove all MainMenuLoop files. Then go to Data/Music/special/ and remove the MUS_MainTheme file.

All original and vanilla game files in your Data folders can also safely be restored with B.A.E. - Bethesda Archive Extractor at Fallout 4 Nexus without having to do any hard re-installs of the game. In this method, you would extract all Fallout 4 BAT game files, drag and drop them in BAE, and extract them to your DATA folder. It would then rewrite all base game files back to their original formats. It does not affect stand-alone mods, but it would affect replacer mods only if they are loose files.