As of about 1:30AM (SK Time) July 13/2014 the server was back online.
I re-installed everything on the server from scratch (Windows, Xitami, Serve-U) on a new hard drive.
I replaced everything in the fansubs.ca folder (as well as a few other files) from the good copy on my main computer instead of what was on the old server hard drive.
But, after all that I found a corrupted ZIP file on the new server hard drive. WTF? ?_?
So after spending about 8 hours on this I'm back where I started. -_-
Apparently the problem may not be the hard drive but something else is corrupting files (especially ZIP files). I had installed WinZIP on the server and found the ZIP files were already corrupted on the server hard drive so it's not getting corrupted in the process of being transmitted out to or across the internet.
If I figure anything else out I'll post it here and on the fansubs.ca page.
There was no impact on E-mail during the maintenance window as that is outsourced to Easy DNS.