Well Shane, that was going to be the second part and maybe part of the first. Supposedly that repair function will also repair the registry and hope fully correct all the registry references from H: to C:.
So if you used Ghost to back up an image of H: to both the other hard drive and CD/DVDs you should be safe and get back to where you are now, if all does not go well.
PM will reassign drive letters, but not to the active drive. You might make the floppies from PM that boot into DOS and then try to reassign the drive letter. Or, boot those floppies and then clean out the drive, reformatting does it, and then the drive letter should go to C:.
Then pull all PCI cards as possible and any other drives but a CD Reader and the hard drive that you want to be C: and the hard drive that has the image. Boot up with the Ghost CD or floppies made from Ghost, if possible, and restore the image. If you have the Ghost floppies, you wouldn't need the other hard drive connected, as the floppies should restore the image from the CDs/DVDs, if you want. If you have the other hard drive with the image connected, go to BIOS and make it the lower boot prioity. I think that the installers always want to make the first priority hard drive the C: drive.
Now when that is all done, it may not boot because the registry is all screwed, so then go back to my first stuff. Try to repair with the Windows CD to see if that fixes the registry references.
If that doesn't do it......................
Do the Files and Settings Transfer Wizard in two steps, Files and the Settings seperately, to the other hard drive. Detach everthing that you can but the one hard drive and reader. If you have onboard audio and or video pull those cards and enable the onboard in BIOS. Then fresh install of Windows. Put the cards back in one at a time between reboots (disabling onboard in BIOS), then the other hard drive with Files, make a restore point and/or Ghost image, transfer files back in, restore point and/or image, then Settings which could still have the H: stuff, if so, you'll have to re-settings manually. Then you will have to reload apps and utilities, but you should have all your data, documents and files. After the bringing the Settings back in the shortcuts may be screwed up but something like Norton utilities and its reg fixer should fix those.