Correct: deactivating the plugin leaves its options in the wp_options table. Deleting the plugin will cause it to clean up after itself.
As for adding functions... you can't really do that... to do all that work you'd basically require the entire plugin. There is apparently a lot of confusion as to how WP handles custom post types since this is one of many similar questions I've gotten: you have to register each custom post type,otherwise WP doesn't know anything about it. And the registration takes on a lot of details to describe the behavior, so it's no something you can quickly bang out... you have to write a lot of code tied to various actions working together in order for it to work -- the process goes all the way to the WP core, so adding a little function to your theme's functions.php file is sorta like cutting off your arm then putting a bandaid on the bloody stump.
When there are bugs with the plugin, file a bug report.