1. I think instead of adding the site menu into the footer, lets make a separate file. So save this file (toolbar-menu.htm) and upload it to your site. Copy the URL to this file.
2. Now save this file (toolbar-options.js), replace the URL (in orange) in these options with the URL from step 1, then replace the options file you have. Also, the part in red has changed.
   
    addToolbarLink.push(["left","frame:250,310","Candara Guardians Site","http://i200.photobucket.com/albums/aa219/Widow-Of-D00m/Emotes/HomePage.png","http://dl.dropbox.com/u/1510510/testing/toolbar-menu.htm"]);
   
   
3. Add this to your footer area html (Control Panel > Custom HTML & Script > Footer Area). Replace the URL in orange with the location of the file from step 2.
   
   <script type="text/javascript" src="http://www.google.com/jsapi"></script>
   <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8/jquery-ui.min.js"></script>
   <script type="text/javascript" src="http://dl.dropbox.com/u/1510510/testing/toolbar-options.js"></script>
   <script type="text/javascript" src="http://www.axiomfiles.com/Files/258012/toolbar.js"></script>
   <link type="text/css" href="http://www.axiomfiles.com/Files/258012/toolbar.css" rel="Stylesheet" media="screen">
   <style type="text/css">
   /* Add Custom Styles here */
   /* Toolbar & Minibar (tbShow) that is visible when the bar is hidden */
   #toolbar, #tbShow {
    background: url(http://i200.photobucket.com/albums/aa219/Widow-Of-D00m/toolbar-blue.png) repeat-x;
    color: #dddddd;
    height: 30px;
   }
   /* Toolbar & Popup Positioning */
   .tbPopupTop { top: 35px }
   .tbPopupBottom { bottom: 35px }
   /* Toolbar image size & spacing */
   .tbMain img, .tbSearch img, #tbHide img, #tbMove img, #tbShow img {
    height: 18px;
    width: 18px;
   }
   /* Search box area & color */
   #toolbar .tbsearch input { background: #333333; color: #dddddd; }
   /* Toolbar Popup */
   #tbPopup {
    background-color: #333333;
    color: #FFC000;
   }
   /* Popup Title */
   .tbPopupTitle { color: #dddddd; font-size: 120%; font-weight: bold; }
   /* Feed Title */
   .gfc-resultsHeader .gfc-title { color: #FFC000; font-size: 120%; font-weight: bold; }
   </style>

<script type="text/javascript">
$(document).ready(function(){
 var max = 30,
  medalsPerRow = 10,
  levels = {
   1  : 'http://guildportal.com/Layout2006/CP/Awards/Star%20Set%201/award_star_bronze_1.png',
   5  : 'http://guildportal.com/Layout2006/CP/Awards/Star%20Set%202/award_star_bronze_2.png',
   10 : 'http://guildportal.com/Layout2006/CP/Awards/Star%20Set%203/award_star_bronze_3.png',
   15 : 'http://guildportal.com/Layout2006/CP/Awards/Star%20Set%201/award_star_silver_1.png',
   20 : 'http://guildportal.com/Layout2006/CP/Awards/Star%20Set%202/award_star_silver_2.png',
   25 : 'http://guildportal.com/Layout2006/CP/Awards/Star%20Set%201/award_star_gold_1.png',
   30 : 'http://guildportal.com/Layout2006/CP/Awards/Star%20Set%202/award_star_gold_2.png'
  },
  /*******************************
   * Don't change anything below *
   *******************************/
  i, c, m, l, s;
 $('.gpWidget-rosterlrg').find('table[id$=_grdRoster]').find('tr').each(function(){
  c = $(this).find('td:eq(0)');
  l = c.find('img[title*="Medal"]').wrapAll('<span class="medals" style="display:none;" />').length;
  s = (l > max) ? max : Math.round(l/5) * 5;
  if (l < 5) { s = 1; }
  if (l > 0) {
   i = $('<span class="allMedals tooltip" title="Click to see all ' + l + ' medals"><img src="' + levels[s] + '"><span class="count">(' + l + ')</span>');
   i.appendTo(c)
    .click(function(){
     m = $(this).parent().find('.medals');
     if (!m.is('.modified')) {
      m.addClass('modified') // make popup medals easy to see
       .find('img').each(function(){
        $(this)
         .addClass('popupMedal')
         .after( '<span class="popupMedalName">' + this.title + '</span><br>' );
       });
     }
     $.facebox(m.html());
    });
  }
 });
 // this code fixes the medals on the character page
 if (window.location.href.match('CharacterID')){
  $('.gpWidget-rosterlrg').find('b:contains("Awarded Medals")').parent().find('img')
   .addClass('tooltip')
   .each(function(i){
    this.title = this.alt;
    if (i % medalsPerRow === 0) { $(this).before('<br>'); }
   });
 }
});
</script>