Registry Mixed UP in Windows XP

I recently added a second hard disk (E to system as part of my backup
plan. I cloned C: to E: a couple of times without incident as well as the
E: to the C:. Somehow along the way the Windows Registry got messed up.
Now neither HD will boot the computer without both HDs are installed. Also,
many functions of the computer are running off the E: instead of C:. I
looked at the Registry and found that there are several hundred entries in
the Registry of both HDs that refer to the E: drive.

How can I fix this problem? I think that I should be able to edit the
Registry changing all references to E: back to C: However I don't want to
take any chances because I don't want to create a situation where the
computer won't boot.

Is there a utility that makes mass changes to the Registry so that I won't
need to change the entries one at a time?

Thanks in advance for any suggestions.