You will need to start reading about the setting and options API, and then pull your CPT and Taxonomies into it.
Have a start here:
-
Class Reference/WP List Table « WordPress Codex
- Custom List Table Example Plugin – A practical example of WP_List_Table in plugin form
-
Administration Menus « WordPress Codex
- Admin Menu Editor Plugin – allows adding, deleting, hiding, and re-ordering of administration items
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