Since the paths are all different, most likely, you're not going to be able to do the combination of partitions with SuperDuper! -- instead, you'll have to make the inital copy of the primary partition with it, and the rest will have to be done, carefully, with Finder.
Once everything's put back together on the backup, in one partition, you can boot from it, check it, and then copy it back to a clean drive...
Sorry I can't give you lots of steps, but I don't know where everything is, and think if you got yourself into this situation you can probably figure out how to get out better than I can!
