How do I resolve missing content type references from uninstalled modules?
this probably is happening because you've deleted the module from sites/all/modules before uninstalling it correctly via drupal / or the module you have installed did not provided the code to uninstall it from database. Based in this, you can try to install the module again and then, disable it first, then uninstall it, and then delete it from the sites/all/modules. And don't forget to clear the cache

If the problem persist, i think you can always delet the tables individually from phpmyadmin.
Let me know if the problem persists. So, then i can analyze it with you