Not really sure why this fixed it, but it did:
function modify_post_content( $content ) {
$screen = get_current_screen();
$post_type = $screen->post_type;
if ($post_type == 'story'){
require_once('regex.php');
$response_array = regex($content);
$content = $response_array['finalString'];
}
return $content;
}
add_filter('content_save_pre', 'modify_post_content', 10, 1);