Just back up the entire folder (plus the ones in /user name/saved games/), reinstall windows, download the installer and start it. After it has started downloading the actual game files (not the installer updates), cancel the download and put all your back ups back where they were. Run the installer again and it should automatically detect any existing files and folders.
If the modules don't appear installed, you can first try installing them from the module manager. If you don't have that option, there is a sticky in the DCS world forum on using the updater, follow the instructions and tell it to reinstall each module (again it should automatically detect any files that you already have before downloading anything missing).
I used this exact same method to for the exact same reasons. Took a bit of effort but worked flawlessly. Just remember to download and run the updater first and get it to start downloading the game files. The game will run fine without doing this (I.E. manually creating a shortcut to the .exe), but it won't appear in your start menu or programs list.