Google not indexing pages via custom 404.php?

I have a large site that I recently ported over to WordPress. Much of the old content is dynamically dumped into the WordPress framework via a custom 404.php page. This works well, but as far as I can tell none of that content gets indexed by Google. Does that make sense? Might it have to do with the 404 header getting sent? And if so, is there a way to fix it?