Windows will not start up. Before I even get to the splash screen I get the following message. "Corrupt or missing file WINNT/SYSTEM32/CONFIG/SYSTEM..." I tried the emergency repair disc, but it did NOT repair this file.

Boot to win2000 cd and try reinstalling, if rescue disk didn't work that is only good option.

Options that may work: Boot with CD/4 floppies - whichever and choose: 1) Setup/repair and allow it to inspect/restore system files; if that fails... 2) Then perhaps an "Upgrade of current installation" approach (in effect it's a re-install over the current version). If this works it will (should...) preserve all current settings; but you may have to re-apply any SP you are currently using. If neither of those work I guess it's reinstall from scratch...? You could install the (true) replacement alongside current version. You end up (briefly) with a dual-boot with the second version as windows (usually), and can delete the original (winnt) version from the drive (via Explorer) once you've set default OS to boot to new (windows) version. Also edit out references to original version from the boot.ini. All apps/utils will have to be installed afresh for new version. Advantage of this rebuild route is that you do not have to wipe the disk; and data will (should) be safe too. Regardless of how you restore/rebuild - once all OK again - renew ERD; keep safe/current.