This script will allow you to create output on all level's of slugs for a custom post type with a custom taxonomy.

wp-custom-taxonomy-permalink-rewrite.php

<?php

/* 
This script will allow you to create output on all level's of slugs for a custom post type with a custom taxonomy. 

Setup the Custom Post Type slug to be the base:

/custom-post-type-slug/taxonomy-term/post-title

For the below code, I'm using a custom post type registered as: recipe
and a custom Taxonomy registered as: recipecategory
make sure you use query_var => true in the setup of the CPT and Taxonomy
for example:

/recipe/chicken/chicken-potpie

Navigation and templates:

/recipes -  archive-recipe.php
/recipe/chicken - taxonomy.php
/recipe/chicken/chicken-potpie - single-recipe.php

*/

function customTaxonomyRewrite() {

	add_rewrite_rule('(recipe)/(.+?)/(.+?)(/[0-9]+)?/?$','index.php?post_type=recipe&slug=$matches[1]&recipecategory=$matches[2]&recipe=$matches[3]&page=$matches[4]','top');
	add_rewrite_rule('(recipe)/(.+?)/?/?$','index.php?recipecategory=$matches[2]','top');
	add_rewrite_rule('^recipe/([^/]*)/?','index.php?recipecategory=$matches[1]','bottom');
	add_rewrite_rule('^recipe/?$','index.php?post_type=recipe','bottom');
	
	
}

add_action('init', 'customTaxonomyRewrite', 10, 0);