Adding the below code to header-diff.php should have removed canonical from my custom pages. But it didn't.. Any help?
<?php add_filter( $wpseo_canonical, __return_false ); ?>
Reference:
http://codex.wordpress.org/Function_Reference/add_filter
and
http://yoast.com/wordpress-seo-api-docs/
Any help Yoast, Joost de Valk