Hi there,
The actual X theme folder is still 4.0.2. You’ll need to first delete it and then extract your uploaded x-4.0.6.zip file (see: http://prntscr.com/83ftbu), you can do it using your File Manager in the cPanel.
As for the WooCommerce notice, it looks like you are using the latest version of WooCommerce that may not be fully supported by X theme at the moment. As per our changelog, the current compatible version of WooCommerce is 2.3.9, so I’d advise downgrading your WooCommerce version to 2.3.9.
Thanks!