Coda-Blue Workaround?

I’m working with a very particular theme called Coda-Blue at https://www.mynaftc.com/. This theme consists of three simple parts – header.php, index.php and footer.php, and basically builds a navigation menu that allows you to scroll like a slideshow through your website’s pages.

I’m running into trouble when I try making certain pages not appear in the website navigation. This theme doesn’t use wp_list_pages or wp_page_menu, but rather uses the following two pieces of code:

<ul class="navigation">
<?php while (have_posts()) : the_post(); ?>
<li><a href="#<?=$post->post_name?>"><span><?php the_title(); ?></span></a></li>
<?php endwhile;?>
</ul>

and …

<div class="scrollContainer">
<?php while (have_posts()) : the_post(); ?>
<div class="panel" id="<?=$post->post_name?>">
<h3><?php the_title(); ?></h3>
<?php the_content(); ?>
</div>
<?php endwhile;?>
</div>

There are certain pages that I don’t want to populate in either the ul class=”navigation” or the div class=”scrollContainer”, but I’m having no luck with coding an exclude command, and I have already tried every plugin in the world, and none work.

I can’t use a wp_list_pages, wp_page_menu or variation their of because it throws off my CSS, and doesn’t synch the menu navigation to the scroll box at the bottom.

Any help here would be greatly appreciated.