Ok in the meantime i have done some diggin around my self. I ended up going thru the class-wp.php file (WP::parse_request). I came up with the following rewrite rule which works with my CPT.
function add_cpt_rules() {
global $wp_rewrite;
add_rewrite_rule(
"showcase/([^/]+)(/[0-9]+)?/?$",
"index.php?showcase=" . $wp_rewrite->preg_index(1) . "&page=" . $wp_rewrite->preg_index(2),
"top");
add_rewrite_rule(
"work/([^/]+)(/[0-9]+)?/?$",
"index.php?work=" . $wp_rewrite->preg_index(1) . "&page=" . $wp_rewrite->preg_index(2),
"top");
$wp_rewrite->flush_rules();
}
add_action( 'init', 'add_cpt_rules' );
showcase and work are my additional CPTs i removed the extra template include function. As WP now grabs the post_type for the relevant template file.
Using Debug This plugin helped a lot. (http://websynthesis.com/fixing-wordpress-404-errors/)
regards,
Arnaud