I think I've found out why it was on D:\ and not C:\ now. I originally started the installation through the Windows 7 install which shows the drive letters Windows 7 uses when selecting an install disk. As I installed it on D:\ it thought that the drive letter should stay the same.
Starting the installation straight from the disk, however, does not give you the list of drive letters so whatever partition you choose it installs on C:\.
I decided to backup all the stuff I use on the server and just do a clean install (IIS was giving me grief as well about me completely changing how I wanted it to host my websites) and hopefully I can put this problem behind me now; trying to fix it "properly" is just to much of a pain.