Remake the HDD contents from scratch, i.e. recreate the partitions, then put on a fresh copy of all the files... In hopes of any bad parts of the drive being recognized and marked/skipped throughout that process.
Seeing how you apparently can't boot anything, your best bets are a) putting the drive into another Xbox and doing it there (with e.g. the Hexen disc), or b) do it in a PC (with XboxHDM).
Honestly, if your time is worth anything to you, don't bother and just try it with a replacement. (Also, if the HDD turns out not to be the issue, you can just swap the old, untouched drive back in.)