by Ken Task.
First of all, congrats! Know it's been painful and has required much of your valuable time away from that for which you use Moodle - teach!
I suspect that the quiz banks themselves might be in need of repair.
Now that server has a lot more resources, don't forget about trying to run the 'health check' tool by URL. Suggestions provided for quiz fixes can be applied via ssh session at the mysql> prompt.
And, IF running a 2.9> version of Moodle, there a script in sitecode/admin/cli/ called fix_orphaned_question_categories.php
whose help says:
Fix orphaned question categories.
This scripts detects question categories that have had their
context deleted, thus severing them from their original purpose.
This script will find the orphaned categories and delete the unused
questions in each category found. Used questions will not be
deleted, instead they will be moved to a rescue question category.
Might be a good thing to run and might result in shorter backup times, more accurate backups which means on the flip more accurate restores as well.
'spirit of sharing', Ken