In answer to my previous question, yes, there is a difference bewteen doing a "repair" before selecing Setup from the CD and selecting "repair" after selecting Setup. The latter triggers the Upgrade path in Win2K, which attempts to save as much as possible as opposed to savaging whatever is on your disk previously.
I'm back up now (mostly); there are still some things to partially or wholly reinstall (e.g. my Orifice 2000 installation was badly hosed), and I have to reapply my SP4 update, but at least I can boot.
Thanks again for all your help and counsel.