I think I might now a way to fix it. Re-install the game but not downgrade it, because the save-game might be a v2. (If you bought the game recently it's probably v2.) If you do so, you will not be able to have any mods installed in the game.
If you want mods you will have to downgrade the game to v1. Then you can use SAMI, I use that for most parts because I mean it's simple. You just download it, install it and the run it. When you install manually it's a bit more work. Then you will have to open the mods with WinRar probably. And you have to get IMG tool...