Populate wordpress menu with link to custom field value (file download)

Try this:

// Filter wp_nav_menu() to add additional links and other output
add_filter('wp_nav_menu_items','add_pdf_to_menu', 10, 2);
function add_pdf_to_menu( $items, $args ) {
    if( $args->theme_location == 'extra-menu')  {

        $pdf = get_post_meta( get_the_ID(), 'mcf_uppsagning-pdf', true );
        if ( $pdf )
            $items .=  '<li><a href="' . wp_get_attachment_url( $pdf ) .  '">Uppsägning</a></li>';

    }
    return $items;
}

Essentially because you’re in the context of the single page get_the_ID() will return the id for the post/page you’re on. If that doesn’t work try using get_queried_object_id() in place of get_the_ID().

EDIT:
changed the above code to return the attachment permalink.