Connor: you seem to be using an “advanced format” drive – like the new drives from WD and Segate. My system’s drive is not an “advanced format” (though several of my media drives are), so I wasn’t aware of this issue.

Setting the boot flag on the protective MBR record is what probably broke your system. Possibly only the GRUB boot code was broken or the entire MBR should be recreated.

To fix, try following the procedure in http://howtoubuntu.org/how-to-repair-restore-reinstall-grub-2-with-a-ubuntu-live-cd

If that doesn’t work, try to recreate the MBR by starting the Ubuntu LiveCD, going into the terminal, running gdisk on your system drive and using the option “n”.