WP_Query, Pagination, static & URL problems

First of all, hello!

So I spent all day trying to fix this and cannot… and it gets more confusing because I am not even sure what the issue is (after finding an undesirable solution).

Problem:
I am using a theme that I downloaded, and to easily get the desired home page I have to use their custom page template as a static home page. After some modifying and testing, I realized that there was no pagination on the static home page. The original also does not contain any pagination, so I did not mess any of their stuff up… I don’t think!

My problem is that I have successfully added pagination, but it fails to link properly. When I click on the various pagination links I tried, it just refreshes the page and shows the same posts. But, there is more! I can get to the other pages containing older posts if I manually type the url https://www.jovialjoystick.com/?paged=2), so I know the pages exist. I just cannot get my pagination to correctly link and when I hover over the pagination, my browser tells me it links to https://www.jovialjoystick.com/page/2/ which DOESN’T exist/work. So that makes me wonder if it is just some url output error that I hope is easily fixed? The undesirable solution is to switch WordPress’ Permalink settings to default, and then the pagination links work, but I do not want that url/permalink structure.

Here is my page’s template code, which the theme developers made (I only removed 2 other loops and added the sidebar) :

<?php
$do_not_duplicate = array();
get_header(); // Loads the header.php template. ?>

 <!-- Begin featured area. --->
 <?php
 $sticky = get_option( 'sticky_posts' );
 rsort( $sticky );

  $loop = new WP_Query(
  array( 'post__in' => array_slice( $sticky, 0, 5 ),
	 'posts_per_page' => 5,
	 'tax_query' => array(
			array(
	   		'taxonomy' => 'post_format',
			'field' => 'slug',
			'terms' => array(
						'post-format-aside',
						'post-format-audio',
						'post-format-chat',
						'post-format-link',
						'post-format-quote',
						'post-format-status',
						'post-format-video'
					),
					'operator' => 'NOT IN'
				)
			)
		)
	); ?>

	<?php if ( $loop->have_posts() ) : ?>

		<div class="flexslider">

			<div class="slides">

				<?php while ( $loop->have_posts() ) : $loop->the_post(); $do_not_duplicate[] = get_the_ID(); ?>

					<figure class="slide">

						<?php get_the_image( array( 'meta_key' => true, 'size' => 'unique-slider' ) ); ?>

						<figcaption class="slide-caption">

							<?php the_title( '<h2 class="entry-title"><a href="' . get_permalink() . '">', '</a></h2>' ); ?>

							<div class="entry-summary">
								<?php the_excerpt(); ?>
							</div><!-- .entry-summary -->

						</figcaption><!-- .slide-caption -->

					</figure><!-- .slide -->
				<?php endwhile; ?>

			</div><!-- .slides -->

		</div><!-- .flexslider -->

	<?php endif; ?>

	<!-- End featured area. -->
<div id="content" class="hfeed">

<!-- Begin excerpts area. -->
		<?php if ( get_query_var('paged') ) { $paged = get_query_var('paged'); }
elseif ( get_query_var('page') ) { $paged = get_query_var('page'); }
else { $paged = 1; }
$loop = new WP_Query(
			array(
				'post_type' => 'post',
				'posts_per_page' => 3,
				'paged' => $paged,
				'tax_query' => array(
					array(
						'taxonomy' => 'post_format',
						'field' => 'slug',
						'terms' => array(
							'post-format-aside',
							'post-format-audio',
							'post-format-chat',
							'post-format-gallery',
							'post-format-image',
							'post-format-link',
							'post-format-quote',
							'post-format-status',
							'post-format-video'
						),
						'operator' => 'NOT IN'
					)
				),
				'post__not_in' => $do_not_duplicate
			)
		); ?>

		<?php if ( $loop->have_posts() ) : ?>

			<div class="content-secondary">

				<?php while ( $loop->have_posts() ) : $loop->the_post(); $do_not_duplicate[] = get_the_ID();  ?>

					<article id="post-<?php the_ID(); ?>" class="<?php hybrid_entry_class(); ?>">

							<?php if ( current_theme_supports( 'get-the-image' ) ) get_the_image( array( 'meta_key' => 'Thumbnail', 'size' => 'thumbnail' ) ); ?>

							<header class="entry-header">
								<?php echo apply_atomic_shortcode( 'entry_title', '[entry-title tag="h2"]' ); ?>
								<?php echo apply_atomic_shortcode( 'entry_byline', '<div class="entry-byline">' . __( 'Published on [entry-published] [entry-edit-link before=" | "]', 'unique' ) . '</div>' ); ?>
							</header><!-- .entry-header -->

							<div class="entry-summary">
								<?php the_excerpt(); ?>
							</div><!-- .entry-summary -->

					</article><!-- .hentry -->

				<?php endwhile; ?>

			</div><!-- .content-secondary -->
<?php
global $wp_query;
$big = 999999999; // need an unlikely integer

echo paginate_links( array(
	'base' => str_replace( $big, '%#%', esc_url( get_pagenum_link( $big ) ) ),
	'format' => '?paged=%#%',
	'current' => max( 1, get_query_var('page') ),
	'total' => $loop->max_num_pages
) );
?>

		<?php endif; ?>

		<?php wp_reset_query(); ?>

	</div><!-- #content -->

<?php get_footer(); // Loads the footer.php template. ?>

I specifically added:

<?php if ( get_query_var('paged') ) { $paged = get_query_var('paged'); }
elseif ( get_query_var('page') ) { $paged = get_query_var('page'); }
else { $paged = 1; }

And this (which I think can solve my url structure in the format, but I am not sure how to do it.)

<?php
global $wp_query;
$big = 999999999; // need an unlikely integer

echo paginate_links( array(
	'base' => str_replace( $big, '%#%', esc_url( get_pagenum_link( $big ) ) ),
	'format' => '?paged=%#%',
	'current' => max( 1, get_query_var('page') ),
	'total' => $loop->max_num_pages
) );
?>

I researched for a long time and just could not get it to work because I am not sure if my urls, code and/or structure is the problem.

Also, I am not using the custom page template how it came. The original contained 2 MORE loops to display gallery archives, so maybe there is a better way of doing what I want? Which is: the sticky post controlled slider with the latest blog posts under it.

I did try to modify the index.php file, so I could just use the main loop… but I could not get the slider to show up properly, which I figured required a lot of theme modifying and dissecting, which I will attempt if I must.