How to delete remain data in WP database after deleting custom post via admin interface

I would take a look at as the example seems to be doing exactly what you want to do in a situation. Your actual code as far as hooking into WordPress looks fine to me, but a key note to remember from the page I linked to is that this event is triggered by post deletion from the database, and not directly from clicking the button to trash a post in the admin panel.

So yeah, test with delete_post() and get back to me.