Virtual servers not working after adding LetsEncrypt certificate

Server Information:

OS: Ubuntu 14.04 Web Server: Apache 2.4.7 Webmin: 1.900 Virtualmin: 6.04

What I have tried/done so far:

Initial attempt: Used certbot instead of the Virtualmin feature to add LetsEncrypt certificate. More info here: https://askubuntu.com/questions/1115202/internal-server-error-after-inst...

Second Attempt: Manually remove /etc/letsencrypt folder and deleting all -le-ssl.conf files then retrying certbot. More info here: https://askubuntu.com/questions/1115487/403-forbidden-error-on-all-sites...

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.