Why doesnt my JavaScript run?
You shouldn't include the ready function, the latest Zen wraps your script in a custom behavior.  Try putting your code directly inside the custom behavior that is already included in the script.js file.

(function ($, Drupal, window, document, undefined) {

Drupal.behaviors.my_custom_behavior = {
  attach: function(context, settings) {

    $(".colorbox-color").colorbox({
      onComplete: function(){
        var bg = $.colorbox.element().data('bg');
        $('#cboxWrapper').css('backgroundColor', bg);
        $('#cboxLoadedContent').css('backgroundColor', bg);
      }
    });

  }
};

})(jQuery, Drupal, this, this.document);