Cook 1 cup sugar in a medium-size heavy skillet over medium heat, stirring constantly, 6 to 8 minutes or until sugar melts and turns golden brown. Stir in butter until melted.
Whisk together flour, egg yolks, milk, and remaining 1 cup sugar in a 3-qt. heavy saucepan; bring just to a simmer over low heat, whisking constantly. Add sugar mixture to flour mixture, and cook, whisking constantly, 1 to 2 minutes or until thickened. Cover and chill 4 hours.
Meanwhile, prepare Cream Cheese Pastry Shells. Spoon caramel mixture into pastry shells, and top with whipped cream.