The error message about mysql_pdo.so is a server configuration problem unrelated to OJS -- probably your php.ini references this file and it doesn't exist on your server. Either way, it's unlikely to prevent OJS from working, but should probably be cleaned up.
As for the failed assertions in DBDataXMLParser.inc.php, this sounds to me like a case where the upgrade is attempting to rename a column, but the column doesn't actually exist. Check your pre-upgrade database to make sure that the following columns exist:
Public Knowledge Project Team