Seeds from 1 vanilla bean or 1 teaspoon vanilla extract
Confectioners' sugar for dusting
1To prepare crust: Whisk whole-wheat flour, ½ cup all-purpose flour, 1 teaspoon granulated sugar and ¼ teaspoon salt in a medium bowl. Cut 7 tablespoons butter into small pieces and quickly rub them into the dry ingredients with your fingers until the pieces are smaller but still visible. Sprinkle almonds over the mixture. Add 3 tablespoons ice water. Toss with a fork until evenly moist. Squeeze a clump of dough: If it stays together, you've probably added enough water. If not, add another tablespoon of water and toss to combine. Knead the dough in the bowl a few times—it will still be a little crumbly. Turn out onto a clean surface and knead a few more times until the dough just holds together. Wrap in plastic wrap and refrigerate for at least 1 hour or up to 3 days (or freeze for up to 3 months).
2When ready to assemble pie: Preheat oven to 375°F.
3To prepare filling: Toss pears with lemon juice in a large bowl. Whisk flour, sugar, cinnamon, nutmeg and salt in a medium bowl. Whisk eggs, milk, butter and vanilla in another medium bowl. Add the wet ingredients to the dry ingredients and whisk to combine.
4Remove the dough from the refrigerator and let stand for 5 minutes to warm slightly. Roll out on a lightly floured surface into a 12-inch circle. Transfer to a 9-inch pie pan (not deep-dish). Trim the crust so it evenly overhangs the edge of the pan by about 1 inch. Tuck the overhang under and crimp the edge with a fork or flute it between your thumb and the side of your index finger.
5Fill the crust with 2 cups of the pears. Arrange the remaining pears in a circular pattern on top of the bottom layer. Pour the custard mixture over the pears.
6Bake the pie until the custard is fully set around the edges and the crust is golden brown, 40 to 45 minutes. Let cool on a wire rack to room temperature, about 1½ hours, then refrigerate for 1 hour. Dust with confectioners' sugar, if desired, just before serving.
To make ahead: Refrigerate crust (Step 1) for up to 3 days or freeze for up to 3 months; thaw in the refrigerator for 24 hours before using. Refrigerate pie for up to 1 day. Dust with confectioners' sugar just before serving.