If you've got replacement drive, have you tried using new drive manufacturer's utility to transfer the o/s?
If you're running XP/2k on this drive, you can set up another drive doing a normal copy and then running fixboot from recovery console. Best done by connecting both the bad and replacement drives to another machine, making sure its set to show hidden & system files, then just copy paste the whole shebang. When complete, put new drive in your machine, boot from install CD and run recovery console. Type fixboot (can do fixmbr for good measure), reboot and it should be ok. Make sure the partition on it is set active after the copy before you move it back to your machine.
(you could also do the copy from from something like BartPE disk in your own machine).