In a small bowl, combine flour and pecans; stir in butter. Press into an ungreased 13 x 9 x 2 inch baking dish. Bake at 350 for 18-20 minutes or until light golden brown. Cool on a wire rack.
In a small heavy saucepan, combine the sugar, cornstarch and flour. Stir in water until smooth. Cook and stir over medium-high heat until thickened and bubbly.
Reduce heat; cook and stir 2 minutes longer.
Remove from the heat. Stir a small amount of hot mixture into egg yolks; return all to the pan, stirring constantly. Bring to a gentle boil; cook and stir 2 minutes longer. Remove from the heat. Gently stir in the lemon juice, butter and lemon peel.
Transfer to a bowl. Cool to room temperature without stirring. Cover surface with waxed paper; refrigerate until chilled.
In a large mixing bowl, beat cream cheese and confectioners' sugar until smooth. Fold in whipped topping. Crumble the baking pecan mixture; set aside 1/2 cup for topping. Just before serving, in a 3 quart trifle bowl, layer 1 cup each pecan mixture, lemon mixture and cream cheese mixture. Repeat layers twice. Sprinkle with reserved pecan mixture. Refrigerate leftovers.