Does anyone know of a way to create a sitemap by using wp_list_pages and have the order by the same orders a custom nav menu?
Using wp_list_pages you can sort order only by:
anything else (like order by custom menu order) you would have to write your own function. But a better way to get it done would be to create a custom walker for it so you could control the output.
Here's a snippet I use to create a sitemap based on custom menu order: http://snipplr.com/view/54404/wordpress-custom-sitemap-shortcode-following-custom-menu-order/