How did the Win 8 repair disc fail you?
You have two partitions with the 'System' designation, this is where the boot files are, with one OS there should only be one. It should be on the same physical hard drive that the OS is on, this way if you remove another HDD your OS will still boot.
Do not delete, erase, move, or format, any hard drive or partition until you get the boot files to the hard drive with W8.
This is assuming you only have one OS installed, Windows 8.
- Disk 0, Backup Drive #1, has the 'System' designation (the boot files) and no OS on this HDD. This is also marked 'Active' which is what the OS installer looks for when you install an OS and will put the boot files there.
- Disk 1, Backup Drive #3 and the C partition with the OS. This should have the 'System' designation (boot files).
- Disk 2, This has a EFI 'System' partition and Backup Drive #2, Your motherboard cannot use UEFI BIOS, so this can be removed later.
Since you just installed W8 and the Backup Drive #3 is empty, the easiest way to fix this will be to disconnect Disk 0 and Disk 2, then re-install W8 on Disk 1.
When you get the option to format the HDD, format it. It's preferable to have the OS partition in the front of the HDD, your Backup partition should be in the back of the HDD.
Once W8 is installed, and running you can shut down and connect Disk 0 and Disk 2.
They will need to have the 'Active' flag removed, the EFI partition formatted.
The detailed procedure can be given when you decide which way to proceed.
The other option would be to disconnect Disk 0 and Disk 2, and run 'Automatic Repair' from your Win 8 repair disc, this must be ran at least three times with re-boots after each run, this will restore the boot files where they should be, on Disk 1.
Read this tutorial for the procedure:
How Run a "Automatic Repair" to Fix Windows 8 Startup Problems
Once the system is booting when only Disk 1 is connected then you can re-connect the other HDDs.
Let us know which way you want to proceed, and we can give more details and answer any questions.