For filling, in a large mixing bowl stir together sugar, the 3 tablespoons flour, vanilla, cinnamon, and nutmeg. Add the plum and nectarine slices; gently toss plums and nectarines until coated. Set filling aside.
For pastry, in a large mixing bowl stir together the 2 cups flour and salt. Using a pastry blender, cut in the shortening or lard until pieces are the size of small peas. Sprinkle 1 tablespoon of the water over part of the flour mixture, then gently toss with a fork. Push moistened dough to the side of the bowl. Repeat, using 1 tablespoon of water at a time, until all is moistened. Divide dough in half. Form each half into a ball.
On a lightly floured surface, use your hands to slightly flatten one ball of dough. Roll dough from center to edges, forming a 12-inch circle. Wrap the pastry around the rolling pin. Unroll onto a 9-inch pie plate. Ease pastry into the pie plate, being careful not to stretch it.
For top crust, repeat rolling with remaining dough. Transfer the filling to the pastry-lined pie plate. Trim the bottom pastry even with rim of pie plate. Cut slits in top crust to allow steam to escape. Place top crust on filling. Trim top crust 1/2-inch beyond edge of plate. Fold top crust under bottom crust; flute edge.
Brush with milk and sprinkle with cinnamon-sugar. To prevent overbrowning, cover the edge of pie with foil.
Bake in a 375 degree F oven for 25 minutes. Remove the foil. Bake for 20 to 25 minutes more or until top is golden. Cool pie on a wire rack. Makes 8 servings.