bones_page_navi and pre_get_posts Action

Question

I'm using the bones wordpress theme, which has the following page navi function:

// Numeric Page Navi (built into the theme by default)
function bones_page_navi($before = '', $after = '', $myquery = null) {
    global $wp_query;
    $bignum = 999999999;

    $maxpages = $myquery ? $myquery->max_num_pages : $wp_query->max_num_pages;

    if ( $maxpages <= 1 )
        return;

    echo $before;
    echo '<nav class="pagination cf">';
    echo paginate_links( array(
        'base'         => str_replace( $bignum, '%#%', esc_url( get_pagenum_link($bignum) ) ),
        'format'       => '',
        'current'      => max( 1, get_query_var('paged') ),
        'total'        => $maxpages,
        'prev_text'    => '<',
        'next_text'    => '>',
        'type'         => 'list',
        'end_size'     => 2,
        'mid_size'     => 1,
        'add_args'     => false
    ) );
    echo '</nav>';
    echo $after;
} /* end page navi */

I have the following action for setting the number of posts that show for the blog archives. It's causing the page navi to return the wrong results sometimes. Here's an example: http://goo.gl/x9Krjp

Here's the action function:

/* =Posts per page for blog
-------------------------------------------------------------- */
function my_post_queries( $query ) {

        // not an admin page and it is the main query
        if (!is_admin() && $query->is_main_query()){

            if( is_home() || is_archive() ){

                $first_page_total= 7; // total number of posts on first page
                $paginated_total = 8; // total number of posts on paginated pages
                $posts_to_skip = $paginated_total - $first_page_total;

                // pagination for custom page(s)
                if ( get_query_var('paged') ) { $paged = get_query_var('paged'); }
                elseif ( get_query_var('page') ) { $paged = get_query_var('page'); }
                else { $paged = 1; }

                // first page query args

                $query->set('posts_per_page', $first_page_total);


                if(is_paged()) {
                    // add paginated query args
                    $offset = (($paged - 1) * $paginated_total)- $posts_to_skip;
                    $query->set('offset', $offset);
                    $query->set('posts_per_page',  $paginated_total);
                }

            }
        }
    }

add_action( 'pre_get_posts', 'my_post_queries' );

If someone could point me in the right direction in terms of why that pagination won't work properly I'd appreciate the help.

Thanks! J.