Windows system files not where they should be

A reinstall is not the only solution, but it would be the fastest and cause you the least problems. Windows is used to having the C: drive as the main partition holding the Operating System files. Some applications likely have this hardcoded, hence the appearance of files like ntldr in the root of C: when its running from D:. A big problem you will run into is that all of your software is now installed and configured to use D:. If you move everything over, there will likely be a ton of programs that will break since they cannot find configuration folders and files. If you want to save your data, I suggest using the Files & Settings transfer Wizard or Windows Easy Transfer (depending on your current version of Windows). Make backups before doing anything drastic though.

"I have a wild idea, which would require good imaging backup of D because it can potentially be destroyed:

Repartition your disk D to make it a bit smaller and move it towards the end of the disk.
Create a new partition at the beginning of D. This will be your new C disk.
Format and transfer all system files to the new partition,
Take out the old C drive and replace it by the D drive. Keep the old C aside.
Boot from this drive. Or use the Windows restore disk to repair the installation on D if required.
Reboot with the old C drive in the drive bay where the old D drive used to be and call it E.
Erase the system files from E.

I take no responsibility whatsoever and do not guarantee that this will work nor how much time you will spend trying to make it work."