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I don't think there are any families missing from the Manual of Nearctic Diptera, but some of them appear as subfamilies - particularly within the Tipulidae, Mycetophilidae and Empididae. If you want alternative keys, then Oosterbroek's key to European families has most, though not all, of the Nearctic families. For initial sorting, I'd be tempted to stick with the old (inclusive) families in any case.