[dnanian]

Safe Boot doesn't have anything to do with SD!, actually. The fact that it wouldn't copy indicates that there's something likely wrong that's pretty basic -- if we can't enable permissions -- something we do with a system tool called vsdbutil -- and we can't repair the database properly, something is messed up with the configuration.

Similarly, repairing permissions doesn't have anythin to do with enabling ownership, but could indicate that you had other significant problems with the drive, with incorrect permissions before you even started. We'd copy those permissions as-is, of course.

It's hard to know what might have happened here, given what you've said. But I'd suggest doing an archive-and-install on top of what you've got to try to clean things up... and rest your PRAM, too...