Were you able to run the MySQL repair? If so, what was the outcome? This is a very common suggestion by support so I would highly suggest that you at least go through the steps outlined in the document.
Are you asking for the configuration file for the system? You should be able to make all of your changes through the UI, but if you want to make sure that they are correct, the majority of this should be in the bmiconfig.xml.
As far as the quarantine port, this should be fine in most cases. Your local system is what is attempting to send the messages to the quarantine. So using the localhost IP for delivery to the quarantine should work. If you want to verify this, after you run the MySQL repair per the document, try to telnet on that machine to the localhost on port 41025 and send a message. You should see it show up in quarantine.
For your SMTP Insertion hosts, if you are having issues delivering messages generated by the system you can make changes here. These would be things like released messages from the quarantine, messages generated by the Brightmail machine (quarantine reports to users), or messages that have been modified by the MTE (Message Transformation Engine).
For quarantine mail, and general mail flow, these settings shouldn't often come in to play.
If you could please run the MySQL repair, and also let me know how much mail is backed up in that spam folder, and then let me know the outcome it would be appreciated. I hope this helps clear things up a little.
Thanks!
Tom