i'm not sure this is the right place but i wanted to point out some issues, i hope will be solved in the stable version, about custom menus.
- Sub pages are not nested like in the normal menu.
It would be nice having that as well as for sub categories and even better if the user could check a "add sub pages / sub categories" in the menu admin panel
- options link_after and link_before are actually after and before text, not sure if options after and before work properly
- i wasn't able to find some sort of wp_set_nav_menu, if it isn't implemented yet i hope it will be in the upcoming version