Gaw, I had posted this one before, but unfortunately, it is gone now. You have to "trick" the installer. I've had this problem myself. This procedure works.
1. Rename your Combat Flight Simulator 3 main game folder. Even by adding just one character.
2. Create a new folder in "C:\Program Files\Microsoft Games\ and name it " Combat Flight Simulator 3 ", exactly.
3. Create new folders inside that new folder named aircraft, weapons, guns, etc.
4. Run the Shared Files self-installer. It will install its contents into this new folder.
5. Move (cut and paste) the newly-installed files that are inside that folder into the appropriate folders inside your old CFS3 main game folder. Make sure not to miss any of them.
6. After they have been transferred, delete the new Combat Flight Simulator 3 folder, and then rename your old Combat Flight Simulator 3 folder back to its original name of Combat Flight Simulator 3. You should be good to go.:d