Help renew an SSL certificate on a now expired Cpanel server license using Let's Encrypt and Certbot-auto

MY WHM/Cpanel license has expired and i did not renew it and don't plan to. I understand a Cpanel installed server changes alot of things and it's always better to do a clean fresh OS install but for my situation I can't. So, let's just first get that out of the way. Because Cpanel is expired and AutoSSL won't work anymore. I got a notification that I have a certificate expiring in 5 days. I installed Certbot-Auto and went through all the steps to set up a Let's Encrypt certificate for this expiring SSL domain. I followed the required steps and I even got the congratulations message and that my certificate has been renewed for 90 days. However, when i go to those SSL check webites. [login to view URL] it still has my old information with Cpanel (Using Comodo) saying my certificate will expire in 5 days. I intend to renew cpanel and now should look at trying to remove what I can from it. Especially the crons and /usr/local/cpanel + /var/cpanel so I don't auto-generate over the top of your existing configurations. I will also need to edit the apache configuration to point to the new certificate (most likely in /etc/letsencrypt/live/DOMAIN/) and reload the webserver for it to use the new certificate. Make sure we setup a cron with certbot-auto renew and with renew-hook/post-hook to reload webserver after it renews