Could you paste the exact output of the commands you ran? Because I’m doubting they actually ran successfully.
You didn’t answer the “can you login as root”. Is that because you don’t know the answer? If you can’t run a shell as root (or don’t have root access through sudo), the instructions on the page you link won’t work.
If you look at the instructions page, there are two alternative Certbot commands given.
For the first one, it says
Running this command will get a certificate for you and have Certbot edit your Apache configuration automatically to serve it.
For the second one, it says
If you're feeling more conservative and would like to make the changes to your Apache configuration by hand, you can use the certonly subcommand:
If you used the second command rather than the first one, you would be expected to edit your own Apache configuration in order to tell Apache to use the certificate that you obtained. (That's what certonly means: only obtain the certificate, don't configure any software on the system to use it.)
You might have conflicting Apache configuration directives for your two different certificates (the old self-signed one and the new Let’s Encrypt one). You can probably find the directives with
