jepper on "custom_pre_get_posts query modification gives 404"

Hi

I've got a nasty problem that i can't seem to get rid of.

In an attempt to remove slugs for a custom post type I've followed this guide:

http://ryansechrest.com/2013/04/remove-post-type-slug-in-custom-post-type-url-and-move-subpages-to-website-root-in-wordpress

We got this working but with updates it somehow broke. Now the WP_Query modifications result in a 404 error page, while the post exists!

So this is my function, with debug code:

function custom_pre_get_posts($query) {
    global $wpdb;

    if(!$query->is_main_query()) {
        return;
    }

    //echo '$query before: <pre>' . print_r($query, true) . '</pre>';

    $post_name = $query->get('category_name');
    //$post_name = $query->get('name');
    $post_name = str_replace(".html", "", $post_name);

    $post_id = $wpdb->get_var( $wpdb->prepare( 'SELECT * FROM ' . $wpdb->posts . ' WHERE post_name = %s LIMIT 1', $post_name ) ); 

    //echo '$post_name: <pre>' . $post_name . '</pre>';

    $post_type = $wpdb->get_var(
        $wpdb->prepare(
            'SELECT post_type FROM ' . $wpdb->posts . ' WHERE post_name = %s LIMIT 1',
            $post_name
        )
    );

   // echo '$post_type: <pre>' . $post_type . '</pre>';

    switch($post_type) {
        case 'product':
            $query->set('product', $post_name);
            //$query->set('name', $post_name);
            //$query->set('p', $post_id);
            //$query->set('page_id', $post_id);
            $query->set('post_type', $post_type);
            $query->is_single = true;
            $query->is_page = false;
            break;
    }

   echo '$query after: <pre>' . print_r($query, true) . '</pre>';

    return $query;
}

which results in a 404 with this query after:

WP_Query Object
(
    [query_vars] => Array
        (
            [category_name] => m-double-you-sachet-whey-isolate.html
            [error] =>
            [m] =>
            [p] => 0
            [post_parent] =>
            [subpost] =>
            [subpost_id] =>
            [attachment] =>
            [attachment_id] => 0
            [name] =>
            [static] =>
            [pagename] =>
            [page_id] => 21037
            [second] =>
            [minute] =>
            [hour] =>
            [day] => 0
            [monthnum] => 0
            [year] => 0
            [w] => 0
            [tag] =>
            [cat] =>
            [tag_id] =>
            [author] =>
            [author_name] =>
            [feed] =>
            [tb] =>
            [paged] => 0
            [comments_popup] =>
            [meta_key] =>
            [meta_value] =>
            [preview] =>
            [s] =>
            [sentence] =>
            [fields] =>
            [menu_order] =>
...
            [product] => m-double-you-sachet-whey-isolate
            [post_type] => product
        )
...
    [is_admin] =>
    [is_attachment] =>
    [is_singular] =>
    [is_robots] =>
    [is_posts_page] =>
    [is_post_type_archive] =>
    [query_vars_hash] => 60f1fdf5aebc76aba270391b0658101c
    [query_vars_changed] =>
    [thumbnails_cached] =>
    [stopwords:WP_Query:private] =>
    [query] => Array
        (
            [category_name] => m-double-you-sachet-whey-isolate.html
        )

)

I've removed some for brevity. Trying to load a post id with a valid ID does not work as well.

How do i go from here?
How do i debug it?

The post is valid and under the id as found by the function

Thanks!