Ive continued to work on this on my own. Im surprised that more people havent been looking for a solution to this. Here is a solution that I worked out that works for me.
In your template.wppa_publication_list.php file in your theme, replace:
<?php $pub->the_title(); ?>
$nolinktitle = ob_get_clean();
echo strip_tags($nolinktitle, '<div>'); ?>
This captures the output of $pub->the_title, turns it to a string, and then strips all html tags, in our case the anchor link, and leaves div tags so we can keep the
<div class="publication_title"> container.
Hope this helps someone.