Is this the way you did repair?
(With the cdrom booting up you select 'install', then you will be prompted to enter the repair console in the next screen. Do not enter the repair console here but continue on by selecting 'install' again. Then you should be presented with the listed operating systems on your pc . This should give you the option to repair those installations. This way it will rewrite over the entire operating system but will leave your installed programs intact. The only difference I have seen using this method is that it wipes out every windows update..)
If this is no good can you install w2k on another partition?