If I understand correctly, you have a SD clone that predates 10.6.3.
If that's the case, once you wipe and get a bootable Mac, and then startup from your external, SD should be a breeze.
If your SD backup is post 10.6.3, and if the problem surfaced after your SD 10.6.3 clone, you may be cloning your problem back to your Mac.
Assuming the former, once you're up and running, use the standalone Combo Updater to go to 10.6.3.
Keep us posted.