Few things has changed in wooCommerce than before. So to remove the shortcode and place our is not possible now. So what you can do is create a new page and place our shortcode there. And the same page should be listed in your menu as shop page.
Also, you can create a 301 redirect with 301 redirection plugin to redirect default wooCommerce shop url to your new shop page where our shortcode is used.
There are also other option with custom template, but it is going to be long process.