I manually imported the sql file to phpmyadmin. The lines I removed from the file seem to only try to import the database. I don't believe they do any sort of updates to it but if they do then I guess my install is messed up anyway.
This will not work because the installer changes several values in the datbase after the import so that ispconfig knows the details of your server configuration. You should uninstall ispconfig with the unistall.php script that you can find in the install folder and then reinstall ispconfig 3.0.1 from the tar.gz