Try deleting the contents of /home/user-data/ssl
then run sudo /root/mailinabox/setup/ssl.sh (assuming you installed MiaB as the root user)
then rerun sudo mailinabox
You should not have the nginx issue as the ssl.sh script solves that issue.
Once that has done, try provisioning the cert(s) in the admin area.
Let me know if this works, or not. Somehow I feel that I am missing a step. 