Well after a good bit of searching I seem to have this working, I hope this helps someone.
<div class="col1">
<?php
if (get_option('woo_show_carousel') == 'true' AND !is_paged()) { include (TEMPLATEPATH . "/includes/featured.php");}
?>
<?php
if (is_paged()) $is_paged = true;
if (get_option('woo_slider_exclude') == "true") $shownslides = get_option('woo_shown_slides');
if(empty($showslides) || get_option('woo_show_carousel') == 'false'){
$showslides = array();
}
$showvideo = get_option('woo_show_video');
$vidtags = get_option('woo_video_tags');
if(!empty($vidtags)) {
$vidtags_array = explode(',',$vidtags);
} else {
$vidtags_array = array();
}
global $wpdb;
foreach ($vidtags_array as $tag_name){
$tag_name = trim($tag_name);
$tagid = $wpdb->get_var("SELECT term_ID FROM $wpdb->terms WHERE name="$tag_name"");
$tagids[] = $tagid;
}
$paged = (get_query_var('paged')) ? get_query_var('paged') : 1;
$taxonomy = 'category';// e.g. post_tag, category
$param_type="category__in"; // e.g. tag__in, category__in
$term_args=array(
'include' => '3,4,5,6,11,14',
'orderby' => 'ID',
'order' => 'ASC'
);
$terms = get_terms($taxonomy,$term_args);
if ($terms) {
foreach( $terms as $term ) {
$args = array(
"$param_type" => array($term->term_id),
'post_type' => 'post',
'post_status' => 'publish',
'posts_per_page' => 1,
'caller_get_posts'=> 1,
'post__not_in' => $shownslides,
'tag__not_in' => $tagids,
'paged'=> $paged
);
query_posts($args);
$home_content = get_option('woo_home_content');
$home_boxes = get_option('woo_home_boxes');
static $counter = 0;
if (have_posts()) :
$full = FALSE;
$width = get_option('woo_full_thumb_width');
$height = get_option('woo_full_thumb_height');
if( $home_boxes == 'On') { $small = TRUE; }
elseif ($home_boxes == 'Off') { $full = TRUE; }
else { $large_posts = intval($home_boxes); }
while (have_posts()) : the_post();
$counter++;
$post_class="full";
if( ($counter > $large_posts OR $small == TRUE) AND $full == FALSE)
{
$width = get_option('woo_boxed_thumb_width');
$height = get_option('woo_boxed_thumb_height');
if( $small == FALSE ) $counter = 1;
$small = true;
if ($counter%2 == 0 ) { $post_class="fr"; }
else { $post_class="fl"; }
}
?>
<div class="post-outer post <?php echo $post_class; ?>">
<div class="post-inner post-alt">
<?php woo_get_image('image',$width,$height); ?>
<h2><a title="<?php _e('Permalink to ',woothemes); ?><?php the_title(); ?>" href="https://wordpress.stackexchange.com/questions/13935/<?php the_permalink() ?>" rel="bookmark"><?php the_title(); ?></a></h2>
<p class="category-head cufon"><?php the_category(', ') ?></p>
<?php if ($home_content == 'false') { ?>
<p><?php echo strip_tags(get_the_excerpt(), '<a><strong>'); ?></p>
<?php } else { ?>
<?php the_content(__('Continue Reading',woothemes)); ?>
<?php } ?>
</div><!--/post-inner-->
</div><!--/post-->
<?php if ($counter%2 == 0 AND $small == TRUE ) { echo '<div style="clear:both;"></div>'; } ?>
<?php endwhile; ?>
<?php endif;
}
}
wp_reset_query();
?>
<div class="more_entries">
<?php if (function_exists('wp_pagenavi')) wp_pagenavi(); else { ?>
<div class="fl"><?php previous_posts_link(__('« Newer Entries ',woothemes)) ?></div>
<div class="fr"><?php next_posts_link(__(' Older Entries »',woothemes)) ?></div>
<br class="fix" />
<?php } ?>
</div>
<div class="fix"></div>
<?php
if (get_option('woo_show_video') == 'true') { include (TEMPLATEPATH . "/includes/video.php");}
?>
<?php
if (get_option('woo_show_talking_points') == 'true') { include (TEMPLATEPATH . "/includes/talking-points.php");}
?>
</div><!--/col1-->