Preheat oven to 350°F Butter and flour 2 9 cake pans.
Beat eggs and sugar together in top of a double boiler until light and fluffy. Transfer to bowl of stand mixer; beat at medium until cool. Add lemon zest, vanilla and butter. Add flour 1/3 cup at a time, beating until well mixed. Pour into prepared pans and bake 40 min or until a toothpick inserted in the center comes out clean.
Meanwhile, heat milk in a saucepan. In a bowl, beat sugar, egg yolks, flour and cornstarch. Add hot milk a few spoonfuls at a time, beating constantly, until about 1/3 of it has been added, after which the contents of the bowl can be added to the saucepan with the vanilla. Cook over medium-low heat until thickened, stirring constantly. Transfer to a bowl, cover with plastic wrap, and refrigerate until cold.
Trim cake layers so they are level. Pour filling on bottom layer, and position top layer over the filling.
Chop chocolate coarsely and place in a microwave safe bowl. Microwave chocolate at 50% (medium) in 30 second increments, stirring after each, until fully melted. Beat cream cheese in mixer at medium speed until soft; reduce speed to low and add confectioner's sugar and chocolate. Beat until smooth, glossy and fully mixed. Spread topping over the top of the cake - do not frost sides. Keep refrigerated until ready to serve.