PROBLEM:

Your cPanel LetsEncrypt integration can not setup SSL certificate:

The system queried for a temporary file at “<a href="http://domain.here/.well-known/acme-challenge/*">http://domain.here/.well-known/acme-challenge/*</a>”, but the web server responded with the following error: 403 (Forbidden)"
Or it shows 404 Not Found page.

SOLUTION:

403
make sure that the directory where are your website files is set with the write permissions (example chmod 750) drwxr-x---
Also that directory should not have immutable bit (lsattr, chattr)
To workaround 404 error, one can try to add following line to the file .well-known/.htaccess
RewriteEngine On
which will break all parent .htaccess rewrite rules