Drain pineapple, reserving juice. Dissolve gelatin in boiling water; add pineapple. Pour into a 13”x9” dish; chill until almost set, about 45 minutes. In a mixing bowl, beat cream cheese and whipped topping until smooth. Carefully spread over gelatin; chill for 30 minutes.
Meanwhile, in a saucepan over medium heat, combine sugar, lemon juice, water, flour, egg yolks and reserved pineapple juice; bring to a boil, stirring constantly. Cook 1 minute or until thickened. Cool. Carefully spread over cream cheese layer; chill for at least 1 hour.