In Windows 7, you should not install to Program Files directories. I don't know if you did this? Anyway, have you tried to simply copy the whole BG2 installation to a new location? And then perhaps change the paths in baldur.ini to that new location?
Hello Ayrus, as said I did not install anything. I simply copied the old game into a new game directory (no, not program files

Alternatively, you could also install BG2 and ToB, let's say to D:\bg2\ (I use that directory), and then apply the official patch. Then rename that installation directory to something else (let's say d:\BG2-vanilla). And now copy or rename your current installation (the one you have modded) to d:\BG2. That way, the registry entries point to that location, and everything should work fine.
This was indeed my alternative solution.
I always keep a vanilla version that way as a backup (well, actually I set all the settings like Debug mode etc so I don't have to do that again), since it's much faster to rename a couple of directories than uninstalling and installing the game(s) from scratch. If I make errors when installing mods, or if the mods conflict in a way that the installation is "broken", I can always revert to that vanilla-version and delete the modded version. Of course, this can take a lot of disk space. But in the end, once you are done with installing mods, you can always remove those backup installations if necessary.
Well, I don't keep a vanilla but completely installed one so I don't need to do all mods all over again. However, perhaps it is wise if I ever want to play CA or TuTu
Will let you know how it worked once I get around to it.
[edit] Okay changing the .ini did not work. Will try the second method later.