Try this
http://forums.pocketplane.net/index.php?topic=15921.0You may be able to move/copy/rename your heavily modded one to a new directory name ifi for no other reason then to have a full backup) then install a new copy to the same directory for registry purposes, BG really doesn't appear to need the reg keys, it seems to help more with autostarting. Then put a shortcut on the desktop to the Tutu'd copy of IIRC bgmain.exe to the desktop, with the starting directory the Tutu directory.
I did that it works for me, I have a BG1/TotSC full install, BGII full install, BG2-Tutu without the CDx directories, on my computer.