I know this thread is a little old now but hopefully this suggestion will help others. Almost everything I found while I was looking into this was really old, so I'm sure the topic could use a refresher. Actually, I figured out a way to create a custom 404.php page without writing any custom php code, or using another theme's template. Instead, I just added custom widget areas to index.php and built my custom content with widgets, which was really easy, even for someone who, like me, doesn't know any php. I describe how to do it here:
http://miscellaniackery.com/solving-...ues-atahualpa/. Hope this is useful to someone!