Ian, with a change in mobo and graphics card, I'm sure that you will have to reactivate the installation. Hopefully you still have the product key handy!
More to your immediate issues, install-nvidia-debian.sh also creates a fresh xorg.conf. You should backup your old xorg.conf although the script also does that, I think. Most hardware are detected at boot but you should be sure your hard disk(s) are the same hda/hdb or fstab should be updated properly.
That's the genius of kanotix.