Why don't you just use the hard drive manufacturer's own software for cloning an old drive to a new one. eg. Maxtor have MaxBlast available on their website as a free download.
Just temporarily connect the new C drive as a IDE slave with the old C drive staying where it is on IDE master. Run the MaxBlast software - select the option to copy old drive to a new one.
Then just disconnect the old C drive and connect the new C drive as IDE Master and the D drive onto IDE Slave.
MaxBlast only works if one of the hard drives is a Maxtor. If your two C drives are different makes check the manufacturers website for their own brand of format software.