We repaired the db a couple of times and corrected most of the problems. I also found that I was on a bit of a wild goose chase in that three of the courses I thought were lost were really never on Moodle to begin with (we are moving about 600 courses from eCollege to Moodle).
But I did discover from this episode that we are not routinely backing up the database structure itself. And I learned that the tape backup we were making each day is just about worthless for this purpose. We are getting that corrected ASAP - installing a automated db backup/archiving program so that we can roll back to a previous time period if needed.
Thanks again for your suggestions. One of the great things about Moodle is the Moodle community.