I am having trouble getting pagination to show up for my custom post type, even though the settings are properly set in the Atahualpa control pages.

I have created a custom post type called "reviews". In order to display all the content I wanted, I also created a reviews custom page template in the theme folder based upon Atahualpa's index.php, but using an alternative WP_Query. Although I have pagination set to appear in Atahualpa, and it does appear on standard posts, but not on my custom post type page. I do have the appropriate hooks in my page template:

bfa_next_previous_page_links('Bottom');

So, how can I connect my custom post type to Atahualpa's logic so it knows to properly display pagination when there are more posts than fit on a page?

I'd have to see the complete file to give you any help.

Sorry for the length of this... And thank you for any help that you can offer. As you can see, all that is changed is that I replaced the bfa_post_kicker() to the bfa_post_footer() function calls with a reference to the template part associated with the post type, and hooked in a custom Query...

All the other Atahualpa functions are working swimmingly on this page, and the multiple posts (standard post type) have the of the next/previous links appearing properly.

More information that I discovered: I do get page navigation for "< Newer" only if I manually go to /reviews/page/2/ by inserting previous_posts_link(), but though there are also "Older >" custom post types, this nav element is not showing up.

<?php
/*
Template Name: Reviews
*/


list($bfa_ata, $cols, $left_col, $left_col2, $right_col, $right_col2, $bfa_ata['h_blogtitle'], $bfa_ata['h_posttitle']) = bfa_get_options();
get_header(); 
extract($bfa_ata); 
global $bfa_ata_postcount;
?>

<?php
$mypost = array( 
				'post_type' => 'cyc_review',
				);

$loop = new WP_Query( $mypost );


 /* If there are any posts: */
if ($loop->have_posts()) : $bfa_ata_postcount = 0; /* Postcount needed for option "XX first posts full posts, rest excerpts" */ ?>
	<div id="cyc_reviews" class="cyc_reviews">
    <?php  if ($bfa_ata['widget_center_top'] <> '') { 
          echo bfa_parse_widget_areas($bfa_ata['widget_center_top']); 
	} ?>

	<?php // Deactivated since 3.6.5
	# include 'bfa://content_above_loop'; 
	// Uses the following static code instead: ?>
	<?php bfa_next_previous_page_links('Top'); // For MULTI post pages if activated at ATO -> Next/Previous Navigation:  ?>

	<?php while ($loop->have_posts()) : $loop->the_post(); $bfa_ata_postcount++; ?>



	
		<?php // Deactivated since 3.6.5
		#include 'bfa://content_inside_loop'; 
		// Uses the following static code instead: ?>
		<?php bfa_next_previous_post_links('Top'); // For SINGLE post pages if activated at ATO -> Next/Previous Navigation  ?>
		<?php /* Post Container starts here */
		
		// ========================================================================================
		// = if it is a review page, then use the review template. otherwise, standard atahualpa. =
		// ========================================================================================
		
		if ( get_post_type( get_the_ID() ) === "cyc_review" ) {
			get_template_part( 'content', 'review' );
		} 
		?>

	<?php endwhile; ?>
	</div>
	
	
	<nav>
	    <?php previous_posts_link('&laquo; Newer') ?>
	    <?php next_posts_link('Older &raquo;') ?>
	</nav>
	
	
	<?php // Deactivated since 3.6.5
	# include 'bfa://content_below_loop'; 
	// Uses the following static code instead: ?>
	<?php bfa_next_previous_post_links('Middle'); // Displayed on SINGLE post pages if activated at ATO -> Next/Previous Navigation: ?>
	<?php bfa_get_comments(); // Load Comments template (on single post pages, and static pages, if set on options page): ?>
	<?php bfa_next_previous_post_links('Bottom'); // Displayed on SINGLE post pages if activated at ATO -> Next/Previous Navigation: ?>
	<?php bfa_next_previous_page_links('Bottom'); // Displayed on MULTI post pages if activated at ATO -> Next/Previous Navigation: ?>
						

    <?php if ($bfa_ata['widget_center_bottom'] <> '') { 
          echo bfa_parse_widget_areas($bfa_ata['widget_center_bottom']); 
    } ?>

<?php /* END of: If there are any posts */
else : /* If there are no posts: */ ?>

<?php // Deactivated since 3.6.5
#include 'bfa://content_not_found'; 
// Uses the following static code instead: ?>
<h2><?php _e('Not Found','atahualpa'); ?></h2>
<p><?php _e("Sorry, but you are looking for something that isn't here.","atahualpa"); ?></p>

<?php endif; /* END of: If there are no posts */ ?>


<?php get_footer(); ?>

Figured it out myself. I had renamed the query variable $loop, and Atahualpa expects it to be $wp-query.