In a large mixing bowl, combine the two packages of instant Jell-O vanilla pudding mix with the 3 cups of whole milk. Whisk together until the mixture thickens, about 2 minutes.
Once the pudding is ready, add in the 1 cup of creamy peanut butter. Blend well until completely smooth. Then, gently fold in the 12 ounces of thawed whipped topping until combined. Set this mixture aside.
Take your 9x13-inch baking dish and spread a thin layer of the pudding and peanut butter mixture on the bottom. Next, place a layer of chocolate graham crackers over the pudding, breaking them as needed to fit.
Spread half of the remaining pudding mixture over the first layer of graham crackers. Sprinkle half of the halved mini peanut butter cups on top of the pudding layer.
Repeat the process by adding another layer of chocolate graham crackers, followed by the remaining pudding mixture and the rest of the halved peanut butter cups.
Finish with a final layer of chocolate graham crackers, pressing down gently. This will create a sturdy base for the frosting.
Spread the 16 ounces of prepared chocolate frosting evenly over the top layer of graham crackers. Make sure to cover it thoroughly for a rich finish.
Cover the dish with plastic wrap and refrigerate for at least 4 hours, or overnight if possible. This allows the flavors to meld beautifully and the graham crackers to soften. When ready to serve, slice into squares and enjoy!