2 Queries on Blog Page, Broken Pagination

We have a page layout that has two queries running. For some reason, the pagination for our main query returns a "Page Not Found" when we try to navigate to page 2. We've tried different methods of offsetting the pages but no luck.

Genesis Support Recommended this: http://www.billerickson.net/code/pagination-in-a-custom-query/. This change added a loop after every entry, so we tried changing add_action( 'genesis_after_entry', 'be_galleries_loop' ) to add_action( 'genesis_loop', 'be_galleries_loop' ). It ran the loop once but the pagination was still broken.

Any help would be much appreciated.

Demo: demo.creativepatience.com/magazine/

home.php code

// Add our first 3 featured posts

add_action( 'genesis_before_content', 'cd_goh_loop', 50 );
function cd_goh_loop() {
	$args = array(
		'orderby'       => 'post_date',
		'order'         => 'DESC',
		'post_type' => 'post',
		'posts_per_page'=> '3', // overrides posts per page in theme settings
	);
	$loop = new WP_Query( $args );
	$count = 0;
	global $post;
	if( $loop->have_posts() ) { ?>
    <div class="mag-home-content">

		<?
		// loop through posts
		while( $loop->have_posts() ): $loop->the_post();
		
		$do_not_duplicate = $post->ID;
		
		if ($count == 0 )
		$image_feat = genesis_get_image( 'format=url&size=home-top');
		else 
		$image_feat = genesis_get_image( 'format=url&size=box-month-image');
		echo '<article class="mag ';
		if ($count == 0 ) echo 'feature';
		elseif (($count == 1 ) || ($count == 2 )) echo 'one-third feature-next';
		else echo 'teaser one-third';
		if( 0 == $loop->current_post || 0 == $loop->current_post % 3 ) : echo ' first';
		endif;
		echo '">';	

	      printf( '<div class="home-mag-image"><a href="%s" rel="bookmark"><img src="%s" alt="%s" /></a></div>', get_permalink(), $image_feat, the_title_attribute( 'echo=0' ));
           printf( '<h4 class="entry-title"><a href="%s" rel="bookmark">%s</a></h4>', get_permalink(), get_the_title());
?>
<div class="entry-content"><?php 
		  if ($count == 0 ) mag_excerpt(500);
		  else mag_excerpt(100);?></div>
<?		echo '</article>';
		$count++;
		endwhile; ?>
        </div>
		<?
	}
wp_reset_query();
}

// Do the rest of the posts
remove_action('genesis_loop', 'genesis_do_loop');
add_action( 'genesis_loop', 'sf_custom_loop' );
function sf_custom_loop() {
global $paged;
/* Excludue the first 3 posts from the main query */
$temp_featured = get_posts( 
    array(
        'orderby'       => 'post_date',
		'order'         => 'DESC',
		'post_type' => 'post',
		'posts_per_page'=> '3'
)
        );
$featured_ids = wp_list_pluck( $temp_featured, 'ID' );

$query_args =  array(
                'post_type' => 'post',  
                'posts_per_page' => '7', 
                'paged' => $paged, 
                'post__not_in'   => $featured_ids
                );
$main_query = new WP_query ($query_args);

//displaying the full query of the page
if ($main_query->have_posts ()) : 
    while ($main_query->have_posts ()) : $main_query->the_post();

	if ($count <= 1 )
		$image_feat = genesis_get_image( 'format=url&size=home-top');
		else 
		$image_feat = genesis_get_image( 'format=url&size=box-month-image');

        		echo '<article class="mag post ';
		if ($count <= 1 ) echo 'feature';
		else echo 'teaser one-half';
		if( 0 == $main_query->current_post || 0 == $main_query->current_post % 2 ) : echo ' first';
		endif;
		echo '">';		

	      printf( '<div class="home-mag-image"><a href="%s" rel="bookmark"><img src="%s" alt="%s" /></a></div>', get_permalink(), $image_feat, the_title_attribute( 'echo=0' ));
           printf( '<h4 class="entry-title"><a href="%s" rel="bookmark">%s</a></h4>', get_permalink(), get_the_title());?>
<div class="entry-content"><?php 
		  if ($count <= 1 ) mag_excerpt(500);
		  else mag_excerpt(200);?></div>
<?		echo '</article>';
		$count++;

    endwhile;
	genesis_posts_nav();
endif;
wp_reset_query();
}