You made this needlessly complicated. If the data was intact on the old drive, you could just have cloned the old drive to a replacement drive.
It would be very difficult (maybe impossible - I'm not sure) to completely eliminate the C drive. You may not be using the OS or any files on the C drive BUT you're booting off the C drive and will need to continue to do so. I'm not aware of any simple way to move the boot sectors to the D drive and have it boot up that way.
If you don't mind continuing to have a C drive then just clone the C drive to the replacement. You can then delete the OS, Documents and Settings, and Program Files folders on the C drive and use if for something else (actually I would recommend you RENAME those 3 folders first to make sure your 2nd OS installation doesn't have any dependencies on the C drive).
If all the C data is still intact when you clone the old drive to the new one then maybe it would be better if you resume booting to the first OS install and remove the 2nd one on the D drive.