I got a error for the CSR key that should be 2048 instead of 1024.
Found this in another post that helped out:
edit the openssl.cnf.master file
(typically it is in /root/ispconfig/isp/conf)
change the "default_bits" from "1024" to "2048"
edit the file config.lib.php
(typically it is in /root/ispconfig/scripts/lib
Change the "1024" to "2048" in the following command:
openssl genrsa -des3 -rand $rand_file -passout pass:$ssl_password -out $key_file 1024 && openssl req -new -passin pass:$ssl_password -passout pass:$ssl_password -key
restart ispconfig (i.e. service ispconfig_server restart)
Waiting for the Certificate from GoDaddy now. Found this topic with a working solutions for GoDaddy. So should also work for me