After a good bit of work I've finished the script to fix corrupt domain entries.
FTN: you should be good now. Please wait until "Server Load" under "Service Status" in your cPanel is below 4, and then try adding the domain again once. You will have to wait 24 hours after adding your domain for it to become active.
Everyone else: please repost your issue in the format described in the first post of this thread.
Admins: with this new script, it's really easy for you guys to deal with these issues, so I'm deescalating this thread.
To fix a corrupt entry, simply run:
sudo /root/python/cli/fix_corrupt_domain.py username domain
For example, for FTN you would do:
sudo /root/python/cli/fix_corrupt_domain.py ftn friendlytechninja.com
The above script will remove all entries for the given domain. Additionally, if it finds other corrupt entries for that user it will pick them up and delete them.