I have a Muscovy duck which tends to have less fat than the more common Pekin duck. Do I need to adjust this recipe at all?

Since the recipe has you removing it every half hour to re-pierce the skin I think you will be able to determine when it is starting to get done. During hour two I would decide if it is time to crank up the heat and let it crisp or let it keep cooking depending on how the fat on the bird looks. But I have only cooked duck quarters never a whole duck.