Hi Ace,
the best "Version" ist to make a copy of an fresch new install of SH3.
It should work to copy your existing Install of SH3 to a new place with other name. After that i would remove SH3 with uninstall exe. Maybe clean registry if you get problems with new install. After new installing make a new copy for having ever a fresh SH3. Then copy back your old intall over your fresh one. Duplicate your "fresh-copy" for every new Supermod. I have, fine working, 5 times SH3. Don`t forget to rename every Version.
I hope i could help.
Best regards