So for those stuck trying to get a working cert for their hostname I did the following
added a virtualhost to server.domain.com to /usr/local/apache/conf.d/vhosts.conf
changed hostname to my desired server.doamin.com hostname and made sure I had created an A record at my domain provider!
I used the auto SSL to generate a certificate and copied the cert and key path to
/usr/local/cwpsrv/conf/cwpsrv.conf
EDIT
ssl on;
ssl_session_timeout 90m;
ssl_certificate /etc/pki/tls/certs/server.domain.com.cert;
ssl_certificate_key /etc/pki/tls/private/server.domain.com.key;
ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
ssl_ciphers HIGH:!aNULL:!MD5;
save and close
replacing the ones already there with the new location
/etc/pki/tls/certs/server.domain.com.cert
/etc/pki/tls/certs/server.domain.com.key
restarted Apache and my server is now green with the correct certificate