My issue is that I continued to create the certificates after i got an error message from Letsencrypt.
What I think you did wasn't to create the certificates (it's the letsencrypt client and server that do that), but instead to set config database entries pointing to a certificate, chain, and key that didn't exist. That would most definitely kill your web server.
The error message given by the client indicates that the letsencrypt server wasn't able to resolve livingnatural.com.au. I don't know why that would be; I'm able to resolve it to 139.218.184.183.
I'd suggest trying again. Do
# cd /opt/letsencrypt
# service httpd-e-smith stop
# scl enable python27
# ./letsencrypt-auto certonly --standalone --email adam@livingnatural.com.au -d livingnatural.com.au
# service httpd-e-smith start
...and stop there, and post the output here. This should be safe to run, as it won't change any of your server configuration. Also post the output of 'ls -l /etc/letsencrypt/live/livingnatural.com.au/'
BTW, do you want more than one host name on the certificate? If I browse to livingnatural.com.au, I'm automatically redirected to
www.livingnatural.com.au; wouldn't you want the www. hostname on the certificate as well? If so, that's easy to do; just add "-d
www.livingnatural.com.au" to the end of the letsencrypt-auto command.