Display Custom Post Type Archive content with Shortcode

Most probably you need a bunch of divs etc duplicated in both archive-custom.php and the shortcode. Identify those divs, and move them into a new template file in your theme, e.g. in part-archive-custom.php.
Then, delete them from archive-custom.php and add a call to get_template_part('part-archive-custom'); instead.

Do the same inside your shortcode.

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