If anyone is still having this problem I have a fairly simple solution. I simply inserted a conditional in the header.php file when generating the nav elements.
<?php if (is_singular('CPT-SINGULAR-NAME')) { ?>
<ul id="projectNav">
<?php wp_list_pages('title_li='); ?>
</ul>
<?php } else { ?>
<ul id="nav">
<?php wp_list_pages('title_li='); ?>
</ul>
<?php } ?>
*Replace CPT-SINGULAR-NAME with your custom post type
After that it was simply a matter of reformatting the css for the former “nav” element into the new “projectNav” element for the new custom post type.
Hope this helps someone, and REALLY hope a more elegant solution is found for this problem soon.
