Adding Read More to Custom excerpts

To show your custom excerpt more text when a post has a manual excerpt, you can filter the excerpt using the get_the_excerpt filter, use has_excerpt() (http://codex.wordpress.org/Function_Reference/has_excerpt) to determine whether the post has a manual excerpt or not, and append the output of your already-existing custom excerpt more function to the excerpt if not. Here’s some code that I tested with your custom excerpt more function above, which does the trick:

function excerpt_more_for_manual_excerpts( $excerpt ) {
    global $post;

    if ( has_excerpt( $post->ID ) ) {
        $excerpt .= new_excerpt_more( '' );
    }

    return $excerpt;
}
add_filter( 'get_the_excerpt', 'excerpt_more_for_manual_excerpts' );