After cloning a drive that has been shown to have bad sectors I wouldn't even bother with any other steps, I would just go repair install and if that fails wipe and reload. You are starting from a position where you know that the system is corrupted and you don't know to what extent - spending hours fiddling would be a waste of effort from that start point. Repairs can drag on forever if you let them and sometimes it is better to take the obvious steps.