Heat oven to 450°F. Place crust in ungreased 9 1/2-inch glass deep-dish pie plate. Press crust firmly against side and bottom. Prick bottom and side of crust with fork. Bake 10 to 12 minutes or until light brown. Cool.
Meanwhile, make bottom layer. In 3-quart saucepan, combine granulated sugar, cornstarch and salt; mix with wire whisk. Blend in lemon juice and cold water, then add egg yolks and blend until smooth. Add butter and gradually stir in boiling water. Heat to boiling over medium heat, stirring constantly. Boil for 2 minutes. Remove from heat and add 1 teaspoon lemon extract, the lemon peel and yellow food color. Partially cool for 30 minutes and pour into the baked pie shell. Refrigerate for at least 30 minutes before adding middle layer.
Make middle layer. In small bowl, beat 1 cup powdered sugar and 1 package cream cheese until smooth. Add milk and stir until well blended. Add pudding mixes and beat 2 minutes until thickened. Fold in pineapple and pineapple extract. Pour on bottom layer. Chill at least 30 minutes.
Meanwhile, make top layer. Beat 1 cup powdered sugar, 1 package cream cheese and 1 teaspoon lemon extract until smooth. Fold in whipped topping and spread on top of cooled middle layer. Refrigerate 2 hours.