To change the link from the whm plugin to your new secure admin panel...
I changed this line in main_menu.php (/usr/local/cpanel/whostmgr/docroot/cgi/lsws/main_menu.php)
Code:
$buf .= '<a href="http://' . $_SERVER['SERVER_ADDR'] . ':' . $admin_port . '/">Admin Web Console</a>';
to
Code:
$buf .= '<a href="https://' . $_SERVER['HTTP_HOST'] . ':' . $admin_port . '/">Admin Web Console</a>';
This makes the admin url to your servers hostname with ssl.