In a heavy saucepan mix your flour, sugar and salt. In another bowl mix your milk with your egg yolks, after blending well pour into saucepan with dry ingredients and cook over medium heat. You'll want to whisk constantly until your custard is smooth and thick. Remove from heat and whisk in your vanilla.
Next pour out your box of vanilla wafers in the bottom of a 13x9 baking dish. Place your sliced banana's over the top of your wafers. Pour and spread your vanilla custard over the top of wafers and banana's and let sit.
In a saucepan mix your other 3 cups of milk with your chocolate pudding mix and cook on medium heat until thick and bubbling. Remove from heat and place spoonfuls of pudding all around the surface and spread to cover surface. Let chill in refrigerator for 1 to 2 hours. Spread coolwhip on top of pudding and toss chocolate on cool whip.