After I changed the WebRoot path from /var/www/openmediavault/ to /media/54bf67db-da31-4c50-bb3c-27140944b223/www/owncloud, this is the new log:
It said>>Error: the configuration object is in use...
It looks like your dns entries are not setup correctly, based on:
"To fix these errors, please make sure that your domain name was entered correctly and the DNS A record(s) for that domain contain(s) the right IP address"
Have you recently made a change to your DNS records? It can take a while to populate.
Also try manually creating the folder and files in your webroot to test and make sure those directories are accessible. For example:
mkdir /media/54bf67db-da31-4c50-bb3c-27140944b223/www/owncloud/.well-known
mkdir /media/54bf67db-da31-4c50-bb3c-27140944b223/www/owncloud/.well-known/acme-challenge
echo "<body>Test</body>" > /media/54bf67db-da31-4c50-bb3c-27140944b223/www/owncloud/.well-known/acme-challenge/test.html
Then go to server.xyz.com/test.html
If you do not get a webpage that says "Test" then your webroot is configured wrong.
(Clean up your test files: rm -r /media/54bf67db-da31-4c50-bb3c-27140944b223/www/owncloud/.well-known)
Otherwise I would post on the Lets Encrypt forums, you will get more prompt and knowledgeable support. My knowledge domain is limited to this one specific use case of Let's Encrypt. If you find anything else please bring back the information so we can try to incorporate it into the plug-in.
p.s. force-renew is coming to the plugin shortly