How do I customize the comment reply link? I'm trying to customize the comment reply link to direct the user to the comment submission form on the same page. I've tried: 

&lt;?php 
$content['links']['#links']['comment-reply']['href'] = '#edit-comment-body-und-0-value';
?&gt; 


in my comment.tpl.php, but no luck. Also I need to add a JavaScript onclick to make the comment body in focus and add the user name of the user being replied to.

What should I do?
Have a look at the code of the AJAX comments module. It does simmilar things. There's a good chance that you can learn from theire code.