I added this to the functions.php under Appearance>Editor and it solved all my trouble. It allows the search to use the categories, and it excludes any out of stock items, as well as displays the search results correctly.

/**
* Adds Category taxonomy query to WP search query
* This addition will make the search more relevant
* @param type $query
*/
function search_filter($query) {
if($query->is_search()) {
// category terms search.
if (isset($_GET[‘product_category’]) && !empty($_GET[‘product_category’])) {
$tax_query = array(
‘taxonomy’ => ‘product_cat’,
‘terms’ => array($_GET[‘product_category’]),
‘field’ => ‘id’,
‘operator’ => ‘IN’,
);
$query->tax_query->queries[] = $tax_query;
$query->query_vars[‘tax_query’] = $query->tax_query->queries;
}
}
}

add_action(‘pre_get_posts’,’search_filter’);

add_action( ‘pre_get_posts’, ‘iconic_hide_out_of_stock_products’ );

function iconic_hide_out_of_stock_products( $q ) {

if ( ! $q->is_main_query() || is_admin() ) {
return;
}

if ( $outofstock_term = get_term_by( ‘name’, ‘outofstock’, ‘product_visibility’ ) ) {

$tax_query = (array) $q->get(‘tax_query’);

$tax_query[] = array(
‘taxonomy’ => ‘product_visibility’,
‘field’ => ‘term_taxonomy_id’,
‘terms’ => array( $outofstock_term->term_taxonomy_id ),
‘operator’ => ‘NOT IN’
);

$q->set( ‘tax_query’, $tax_query );

}

remove_action( ‘pre_get_posts’, ‘iconic_hide_out_of_stock_products’ );

}

Hello, I have the same issue. Can you please describe how to fix it? Love the theme so far. Thanks!