pre_get_posts and search query for admin

Have you tried it with add_action instead of add_filter ? 

add_action('pre_get_posts', 'search_custom_fields');

Is public set to true for your post_type?

And for use on in admin, try: 

if ( is_admin() && $query->is_main_query() ) {
    if ( $query->is_search ) {
       //etc.

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