Richard, thanks for the feedback. I think the problem was that the Centos hostname was something completely different. I changed that to match the DirectAdmin settings, ran through the scripts you recommended again, and the empty caroot cert problem resolved.
I'm having trouble getting an SSL cert on the root domain of the my server hostname.
I've been getting this error message:
Account admin with domain rootdomain.net has an empty caroot cert
The file:
/usr/local/directadmin/data/users/admin/domains/rootdomain.net.cacert
belonging to account...