I'm very sorry that your site got deleted when you removed the domain pointers, we would surely have made notes about it if it had occured during our testing, at no point have adding/removing a domain pointer caused any alterations to my files.
As for migrating the emails, not sure there is an easy way. One way would be to login to the webmail using the default domain account, mark all mails (or do it in batches if there's a lot of them as there's a size limit on import), then under "more" at the top far right chose download. This gives you the option to download a archive of all messages, use the maildir option for best result.
Then log into the webmail for the custom account and under the same "More" link you find the import option.
You could probably achieve the same with a mailclient on your computer as well.
As for the connection, those are the settings I use (though I'm on x11 so obviously I have the x11 server address). Using ssl/tsl as connection security, password authentication, full email as the user for both incoming and outgoing.