Place egg yolks in a large mixing bowl; beat until frothy. Add 1 cup sugar, flour, and butter; beat well. Stir in milk, 1 teaspoon vanilla, and nutmeg. Pour mixture into pastry shell. Bake at 325° for 50 minutes or until a knife inserted in center comes out clean.
Beat egg whites (at room temperature) and cream of tartar until foamy. Gradually add 1/2 cup sugar, 1 tablespoon at a time, beating until stiff peaks form and sugar dissolves. Beat in 1 teaspoon vanilla. Spread meringue over filling, sealing to edge of pastry. Bake at 350° for 10 minutes or until meringue is lightly browned. Cool before serving.