The links arent working because you removed the javascript function from the top of layout.tpl.php that controlled opening the window.
Insert the following code below the link to the style sheet in your layout.tpl.php file and see if that helps.
Code:
<script type="text/JavaScript">
{literal}
<!--
function MM_openBrWindow(theURL,winName,features) { //v2.0
window.open(theURL,winName,features);
}
//-->
{/literal}
</script>