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The process for migrating to a new self-hosted server is similar to the process of migrating your OmniFocus data to the Omni Sync Server (described in the linked support article):
  1. Sync all your devices
  2. Sync one device to your new server
  3. Sync your other devices

The difference is that you'll sync to your own server in steps 2 and 3 instead of syncing to ours, so in Step 2 you'll open Sync Preferences on your iMac and switch the radio from "Connect to an existing database" to "Keep the sync database on this Mac". It will prompt you for a new password for your new sync server, after which you should sync your iMac and then set up your iPhone to use the new server and sync it also.

Hope this helps!