Multiples issues suddenly with our 2 months developing site

Okay, we're facing a couple of issues with a client's site that we're almost officially oppening.

In fact opening was deferred coz of this problems.

1.- MySQL: Suddenly MySQL started to be overloaded with some store links, main main store (shop) and server needs about 30 seconds to serve 45 articles. Server is powerful, and there shouldn't happen this. But also we're facing issues cloning site with All-in-one plugin, or cloning site via softaculous, so there's any problem with the DataBase. Keep in mind that is a site large in size (95% product images), but DB is less than 200MB. We're an agency, and out techs can't help us inside WP. how to handle this ?
2.- The WooCommerce cart: Seems that the top cart icon never end spinning, we checked it all ! and nothing , we can't understand why this suddenly happens. How to fix this ? Detail: if we move this site to another server this works.

This is a cPanel server, owned by us, it's q powerful server with a lot of cores and RAM, fast SSD disks, and almost empty. We have multiple WP and WC sites in it and they don't have any problem, all goes fast and smooth.

What do you guys suggest me ?