This way: https://quickbox.io/wiki/install-lets-encrypt-on-your-seedbox/
I also used mydomain.blah and then www.mydomain.blah in that one line. Perhaps that is it. I just tried to reinstall it, and now it's broken.
It can never locate that file on the last step, so I created an empty file. It was still working OK as far as the cert. But still no dashboard access.
This last time I reran the install, I used another name instead off "www" now it is broken and certs are not working.
It may be quicker to start again, but I get the same errors with Let's Encrypt on BOTH Dedi Boxes running Ubuntu 16.0.4.