I'd start with editing c:\boot.ini to mention only d: as a boot device. That's the way to get rid of the question. Then reboot, try if it works and see if you can delete the Windows folder (followed by all other folders) from c:.
http://support.microsoft.com/kb/289022 tells you how.

But some programs (and you only know which one when it's too late) don't like to have Windows on another drive than c:. So it's more safe to complete your installation on c: and get rid of the installation on d:.
Anyway, your choice.