It returns that the cert is installed but that I need to install an intermediate/chain certificate to link to a trusted root certificate. If I replace the cert.pem with fullchain.pem it returns no ssl installed.
The equivalent files produced by Certbot / letsencrypt will be named
fullchain.pem
chain.pem
You say that it “returns no ssl installed” but I don’t recognise this message. Can you flesh that out a bit more, what message exactly are you seeing, and where ?
If yourdomain_com.crt is the leaf cert, which I’m not certain of, then the exact equivalent would be cert.pem (though using fullchain.pem is preferable for almost everyone).