Do you have an Email_Templates directory in your WA_Universal_Email directory? Universal email will use the templates in that directory to create the emails. These templates would be coded in html.
For example the $MailBody creation should look like this for the email template contactus.php:
//Start Mail Body
$MailBody = $MailBody . "";
ob_start();
require_once(dirname(__FILE__) . ("/Email_Templates/contactus.php"));
$contents = ob_get_clean();
$MailBody = $MailBody . ($contents);
$MailBody = $MailBody . "";
//End Mail Body
What were the steps you took to set up your Universal Email?