Third Attempt: Following the guide here: How to Use Let’s Encrypt SSL Certificate Automatically in Virtualmin / Webmin, I have managed to overwrite the certbot certificate that I initally tried adding with the Virtualmin generated certificate and also successfully redirected my site from http to https automatically. But now the error has changed from 403 to Internal Server Error 500 for this particular site. The other non-sll sites all redirects to the above site instead. Please help me.
It turned out to be a combination of multiple issues. But, we’re switching to certbot for new installs in a day or two (because wildcard certs aren’t supported by the mini client we currently use, and it needs to be updated, anyway), so we’re looking into making it a cleaner/clearer migration process.