This items:
"copy the DB before the server tanked" (as opposed to mysql dump)
and
"fresh copy of the install and had it reference our restored DB" (without editing the sql dump for new location?)
and
"didn't copy over the moodledata folder" (the biggy!)
Is the problem. There a reason 'didn't copy over the moodledata folder'? Unfortunately, that's one of those key pieces in migrating/moving a site.
All those DB references to files are in the DB are hash code. Moodle also creates folders/directories and filenames using the hash code ... *unique as of the time created*. Only a uber MySQL DB Admin might be able to clean that up, I would think.
But there is hope ... the backups you run maually appear to 'clean up' the DB. Just to test how well, have you attempted restore of one of those backups? Getting everything ... including users/grades/etc?
If that backup restores properly, then the 'easiest' way to clean everything up might be to backup the courses one at a time and restore them.
Yes, I know that's 80+ courses! No 'easy button' there!
'spirit of sharing', Ken