shud think so ->
(a) elgg_register_menu_item ('whatever',...) = followed by
(b) elgg_view_menu ('whatever',...)

and ' An additional hook is the 'prepare', 'menu:<menu name>' which enables plugins
 * to modify the structure of the menu (sort it, remove items, set variables on
 * the menu items) ' [@core comments]

Something like this will work

        elgg_register_menu_item('topbar', array(
            'name' => '......',
            'href' => "/.....",
            'text' => elgg_echo('.....'),
            'priority' => 101,
            'section' => 'alt',
        ));

Thanks for your help.

I have the "alt" section setup, but I don't know how to view the menu without viewing all sections, I just want the one. I understand I can "prepare" the menu, but don't know how to go about doing so.

Just realised it's even simpler than that, just put a condition around the original elgg_register_menu - happy days, thanks.