What do you mean by "finish federation"?

Generally, individual activities (subscriptions, posts, comments, votes, etc) are federated within less than a minute of them being created. Your instance learns about other instances e.g. from votes seen on other instances. You'll need to start subscribing to some communities on other instances to get started. You may want to check out Lemmy Explorer or Lemmy Community Browser to find communities and Lemmy Federate to automatically subscribe to other communities and get content sent to you.

The allowed instances list means that the instance will only connect to those instances and will refuse to send activities to any other instance.

Allowed instances is an exclusive list of servers you want to federate with. Leaving it empty means it's not in effect.