Pagination Links not working from index in custom template

Ok so I have built a custom theme and realized I needed pagination. The site runs off of a custom post type as well as the default “Post” post-type.
I’ve read this [ http://codex.wordpress.org/Function_Reference/paginate_links ] and have tried it every which way and the links don’t appear.

I have also read through these forums and got some tips about globalizing $paged and putting it into the query etc and the pagination still doesnt show.

My code is below – any help would be muchly appreciated.

<?php
	global $paged, $wp_query;
	get_header('home');

	$paged = ( get_query_var('page') ) ? get_query_var('page') : 1;

	$awk_title = '';

	$all_args = array(
		'post_type' => 'awk_firstfruits',
		'posts_per_page' => 2,
		'paged' => get_query_var('paged'),
	);

	// array( 'awk_authors', 'awk_story', 'awk_resrouces',
	// 'awk_firstfruits', 'awk_media', 'awk_calendar'

	$featured_args = array(
		'post_type' => array( 'awk_featured'),
		'order' => 'ASC',
		'posts_per_page' => -1
	);

	$authors_args = array(
		'post_type' => 'awk_authors',
		'posts_per_page' => 1
	);

	$story_args = array(
		'post_type' => 'awk_story',
		'posts_per_page' => 10
	);

	$resources_args = array(
		'post_type' => 'awk_resource',
		'posts_per_page' => 10
	);

	$media_args = array(
		'post_type' => 'awk_media',
		'posts_per_page' => 10
	);

	$calendar_args = array(
		'post_type' => 'awk_calendar',
		'posts_per_page' => 10
	);

	if ( is_front_page() || is_page('archive') ) {
		$query = new WP_Query( $all_args );
		$feat_query = new WP_Query( $featured_args );
		$awk_title = 'One New Man Updates';

	} elseif ( is_page('Out Story') ) {
		$query = new WP_Query( $story_args );

	} elseif ( is_page('store') ) {
		$query = new WP_Query( $resources_args );
		$awk_title = 'Resource Center';

	} elseif ( is_page('donations') ) {
		$query = new WP_Query('pagename=donations');
		$awk_title = 'Donations';

	} elseif ( is_page('authors') ) {
		$query = new WP_Query('pagename=donations');
		$awk_title = 'Author Bio';

	} elseif ( is_page('first-nations-declarations') ) {
		$query = new WP_Query('pagename=first-nations-declarations');
		$awk_title = 'First Nations Declarations';

	} elseif ( is_page('our-story') ) {
		$query = new WP_Query('pagename=our-story');
		$awk_title = 'Our Story';

	} elseif ( is_page('our-roots') ) {
		$query = new WP_Query('pagename=our-roots');
		$awk_title = 'Our Story';

	} elseif ( is_page('statement-of-faith') ) {
		$query = new WP_Query('pagename=statement-of-faith');
		$awk_title = 'Our Roots';
	} elseif ( is_page('contact-us') ) {
		$query = new WP_Query('pagename=contact-us');
		$awk_title = 'Contact Us';
	} elseif ( is_page('brochure') ) {
		$query = new WP_Query('pagename=brochure');
		$awk_title = 'Brochure';
	} elseif ( is_page('site-map') ) {
		$query = new WP_Query('pagename=site-map');
		$awk_title = 'Brochure';
	};
?>

<?php if( is_home() ) : ?>
<aside id="slider" class="gradient">
	<div id="images">
		<?php
			if ( $feat_query->have_posts() ) : while ( $feat_query->have_posts() ) : $feat_query->the_post();
		?>
			<figure class="image">
				<h3><a href="<?php echo $cfs->get('slide_link'); ?>"><?php the_title(); ?></a></h3>
				<?php
					if( has_post_thumbnail() ) :
				?>
					<a href="<?php echo $cfs->get('slide_link'); ?>">
						<?php the_post_thumbnail('frontpage-slider'); ?>
					</a>
				<?php
					endif;
				?>
			<figcaption>
				<p>
					<?php the_content('Read More…', false); ?>
				</p>
			</figcaption>
		</figure>
		<?php endwhile; endif; wp_reset_postdata(); wp_reset_query(); ?>
	</div>
</aside>
<?php endif; ?>
<header class="main-nav">
	<?php wp_nav_menu( array( 'theme_location' => 'main-menu', 'container_class' => 'main-nav clearfix' ) ); ?>
</header>

<!-- INDEX TEMPLATE -->
<section id="content">
	<header>
		<h1><?php echo $awk_title; ?></h1>
	</header>
	<?php if ( $query->have_posts() ) : while ( $query->have_posts() ) : $query->the_post();
		enable_more();
	?>
		<article <?php post_class(); ?>>
			<?php
				if( has_post_thumbnail() ) : ?>
					<figure class="thumb border">
						<a href="<?php the_permalink(); ?>">
							<?php the_post_thumbnail('frontpage'); ?>
						</a>
					</figure>
					<div class="text-cont">
						<h1 class="post-title">
							<a href="<?php the_permalink(); ?>">
								<?php the_title(); ?>
							</a>
						</h1>

						<?php
							the_content('Read More');
						?>
					</div>
			<?php
				else :
					echo '<h1 class="post-title">';
					echo the_title();
					echo '</h1>';
					the_content();
				endif;
			?>

		</article>
	<?php
		endwhile;

                $big = 999999999;

                echo paginate_links( array(
	        'base' => str_replace( $big, '%#%', get_pagenum_link($big) ),
	        'current' => max( 1, get_query_var('paged') ),
	        'total' => $wp_query->max_num_pages,
	        'mid_size' => 5
	    ) );

		else:
	?>
		<p><?php _e('Sorry, no posts matched your criteria.'); ?></p>
	<?php endif; wp_reset_postdata(); wp_reset_query(); ?>
</section>

<?php get_sidebar(); ?>
<?php get_footer(); ?>

Thanks!