Your management tools are quite similar to what I use. Ansible, terraform for disaster recovery and development cloud systems, several approaches to backups (duplicity+gpg, rsync), ansible+docker for updating certs, VpnCloud for VPN, docker containers for various things.

Main app is Clojure, so I run a native JVM. Database is fully distributed, RethinkDB, now working on moving to FoundationDB.

The important thing is not to manage anything manually, e.g. treat physical servers just like any other cloud server. It shouldn't matter whether it's physical or virtualized.