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What's the best practice to set-up SCDF server for Failover? I am talking about SCDF server itself. Not the stream and Tasks that you deploy in SCDF. I am planning to use Kubernetes as the runtime.

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Depending on the runtime platform of your choice, you can scale multiple SCDF server instances and with a load-balancer in front, you'd be able to route the traffic among server instances. The idea is that you'd have a backup (server) instance to serve the traffic under failure scenarios.

That said, in Kubernetes, the replication controller keeps track of the pod that's running the SCDF server and upon failure, it automatically creates a new pod to re-establish the server operation, anyway.

Similar capability is also available for PCF, Mesos, and Yarn implementations of SCDF.