Locate and delete this span code:
<span><a href="javascript:void(0);"
onclick="window.open( '<?= $site['url'] ?>presence_pop.php' , 'Presence', 'width=224,height=600,toolbar=0,directories=0,menubar=0,status=0,location=0,scrollbars=0,resizable=1');"
><?= _t('_RayPresence') ?></a></span>
Refresh your site page and it should go away. I suppose if you needed a static link on your page, this is the area you could/would place it as an FYI.
it is also wise to list in a file on your pc, what functions you have changed and their file and line number, so you can see at a glance what might be affected with upgrades in the future.
Can you tell how much of a newbie I am? ;)