That's correct indeed. Certbot uses the port 80 virtualhost from the corresponding configuration file and uses it as a template to generate the port 443 https virtualhost, which it places into its own configuration file with a filename based upon the original, but with -le-ssl suffixed (before the .conf extension).
Strictly speaking the two virtualhosts (HTTP port 80 and HTTPS port 443) can also be configured in the same configuration file, but that's not how Certbot works and I recommend using a single method and keep using that method. Now that Certbot already has "chosen" the separate configuration file method, I'd recommend to stick with that.
But duplicate virtualhosts (i.e., the same port and the same [set of] hostnames) is always bad, whether that's in a single configuration file or separate files.
Another strange thing is that there's only a file ares.crucis.net-le-ssl.conf for a HTTPS port 443 virtualhost for ares.crucis.net, but there is not port 80 configuration file for that hostname? And that particular file has an alias configured for crucis.net, which is also double with the vhost from the file crucis.net-le-ssl.conf?
You really should straighten out those files and configurations
The FQDN for the host is ares.crucis.net. That entry was created while I was building the email server (postfix/dovecot) for TLS. After I got the mail server running, I started building the webserver.
Relearning how to build linux servers using current software and systems, has been interesting. My previous server was CentOS 6.5.
A question. Can I just edit the crucis-court.com-le-ssl.conf to reflect the correct aliases and cert locations? Else, how can I remove the incorrect entries to allow me to recreate the files correctly?
Yes, you should manually edit crucis-court.com-le-ssl.conf so it only contains the port 443 HTTPS virtualhost. When you do, make sure the port 80 HTTP virtualhost you're about to remove is not (significantly) different than the port 80 HTTP virtualhost in crucis-court.com. If there is a significant difference, you need to find out why that is and which virtualhost is actually correct.
Next question is: where did ares.crucis.net.conf go? Why is there only a ares.crucis.net-le-ssl.conf left? Where did the port 80 HTTP virtualhost go?
And after that you should address the question raised by @rg305 why your certbot certificates output shows so many certificates of which many (if not all) are actually duplicates. You should probably also tidy your Certbot certificates, probably just into a single certificate, maybe 2.
And with regard to the initial question about the failing Apache: simply change the /etc/letsencrypt/live/ares.crucis.net-0001/ in ares.crucis.net-le-ssl.conf to /etc/letsencrypt/live/ares.crucis.net/ in the two places it's mentioned (for fullchain.pem and privkey.pem).
In the end this is, frankly, all quite simple and basic webserver and certificate management.
