It looks like you should be able to edit the WA_UniversalEmail/Email_Templates/Registration.php page and add the following code to include the link to the users confirm page:
<?php echo($WAGLOBAL_Root_URL); ?>users_confirm.php?ID=<?php echo($row_WAATKusers['UserID']); ?>&code=<?php echo($_SESSION['randomConfirm']); ?>
everything else looks to be in place.