Preheat the oven to 375°F Lightly butter a 2-quart baking dish. In a large pot, boil the potatoes in enough water to cover until tender, about 15 minutes. Drain.
Meanwhile, melt the butter in a skillet over medium heat. Add 1/2 cup of the brown sugar and cook until melted. Add the lemon and orange juice and bring to a boil. Simmer until the lemon peel is tender, about 5 minutes. Stir in the nutmeg.
Peel the sweet potatoes and slice 1/2 inch thick. Arrange half of the slices in the prepared dish. Layer with half of the salt, pepper, lemon slices and their syrup. Repeat the layering, then sprinkle the top with the remaining 1 tablespoon brown sugar.
Bake the gratin, uncovered, until the syrup is bubbly and the potatoes are lightly browned on top, about 35 minutes.
Do Ahead Refrigerate the unbaked gratin, covered with foil, for up to 2 days. Bake covered for 15 minutes, then uncovered for 30 minutes.