Black admin bar is being hidden by page elements

The styles for the admin bar are generally printed in the head of the site, so perhaps your CSS code is being undone as the printed styles for the admin bar appear after your included style sheet.

Maybe by using the wp_head action you can stop this, placing something like this in your functions file may do the trick:

function modify_admin_bar_css() { ?>
    <style type="text/css">
        #wpadminbar {
            z-index: 99999;
        }
        /* Plus any other styles you may need to add for the menu */
    </style>
<?php }

add_action( 'wp_head', 'modify_admin_bar_css' );

Alternatively you can try to use the !important declaration in your CSS, like so:

#wpadminbar {
  z-index: 99999 !important;
}
/* Plus any other styles you may need to add for the menu */

Note though, using !important in CSS isn’t generally advised so you should always use this sparingly.