Comment box in new window

I'm having so much hassle with the comment.php page. In the event that I can't work out how to fix it I've come up with another idea: the page works OK if I use it as a standalone page but not when I include the code into an existing page on my site.

So, how could I modify it so that the comment.php page loads up as a new window, resized to fit the form it contains, which then closes open submitting the comment and then redirects to the existing index.php page (ie. not in the new window)?? I know it can be done with Javascript but I'm not sure what needs to be altered with the Guestbook to make it work.