"Just use "cp -a ..." - IMHO "dd" is not a good way to copy partitions. You've discovered one of the reasons."
I'm giving this a try as I type this as "cp -a / /mnt". However, since /mnt falls under "/", I expect it will fail. So, I'll probably need to do this from a liveCD, right? The disk already has an MBR, I think, from my previous disastrous exploits.
Will I need to do anything special to make it bootable, or are you saying that I just need to install grub? I'm kinda lost on that point.