Companies with corporate licensing will see drive cloning performed since they many identical systems. For the average desktop it's simply far easier to perform a clean install to insure the best results as well as the new mbr needed. When going to install Windows on the second drive the first should be unplugged already however.
Otherwise you end up with C being D instead since the boot information will be on the first drive not the second with the fresh copy of Windows. I ran into one recently when forgetting to unplug the ide drive where Vista is on when installing XP on the first of tow satas. Windows Explorer listed the drive there as D.
(Unplug the ide drive and reinstall Windows all over again...