After you reinstall windows to your harddrive, assuming it is not a SATA, and assuming you are formatting them, it should automatically be the new C: drive. I would make sure the partion you are using is the first partition on the drive.
On my SATA drive, I have to unplug all the other drives before I install Windows, otherwise my computer sets my SATA to D:. After Windows is installed I replug in the drives so Windows can detect them.
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