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I had the same problem yesterday didn't know which option to choose, but then I read that the Omni Sync Server just uses WebDAV.

Therefore on the iPhone just do the following:

1. Open the OmniFocus Sync Preferences.
2. Select the Advanced (WebDAV) option.
3. In the Location field, put in your sync url.
4. Click the Sync Now button. It will then ask for your username and password.

That should be it, worked fine for me.