Custom Post Type shows pagination (w/404) or posts_per_page query, but not both

Question

I have a custom post type of gallery, and I'm using a template for the archive of page-student-gallery.php. My admin settings for posts shown is 5, I'd like it to show 9 on this page which only contains gallery items.

I've been able to manage the query where it can show EITHER 9 posts OR 5 posts with pagination at the bottom, which leads to a 404 error. I've been checking out code for doing this, but everyone seems to have a different way of going about fixing the problem, and none of the solutions are working for me.

My code for the archive page:

<?php 
$paged = (get_query_var('paged')) ? get_query_var('paged') : 1;
$query = new WP_Query(array(
    'post_type' => 'gallery',
    'paged' => $paged
   //'posts_per_page' => 9
));           
while( $query->have_posts() ) : $query->the_post(); ?>

<article class="oneThird gallery">...</article>

<?php endwhile; ?>

<ul class="pcount">
    <?php wp_pagenavi();
      wp_reset_postdata(); ?>
</ul>

My attempts at using pre_get_posts:

add_action('pre_get_posts', 'show_more_posts');
function show_more_posts($query){
    if($query->is_post_type_archive('gallery') && !is_admin() && $query->is_main_query() )
       $query->set('post_type', 'gallery');
       $query->set('posts_per_page', '9');
};

I'm really confused at this point. What is the best way to implement this kind of setup?

Answer 1

user5477769 reports in the comments of the original post, that the problem has been solved:

I was following Custom Post Type UI instructions but it seems it led me astray. Creating a archive-gallery.php with a vanilla Loop, along with removing is_main_query has solved all problems, and the pages now show with 9 posts and correct pagination.