Preheat your oven to 325 degrees F.
For your brownie batter: Melt your butter in a medium (or large) heatproof bowl over a pot of simmering water.
While the butter is melting, whisk the cocoa powder, sea salt and sugar in a separate bowl. (The sugar and salt will work as abrasive agents to get any lumps out of the cocoa.) Whisk the cocoa/sugar/salt combo into the melted butter until the sugar has dissolved fully. The mixture should look like fudge and pull away from the bowl into a ball. Take off the stove and set the pan on a dishtowel on your counter. Allow the fudgy mixture to cool down until it's warm, but not hot anymore.
While that is cooling, line the bottom and sides of your 9 by 13-inch baking pan with parchment paper or foil. You want to leave about 4 inches of overhang on the 2 opposite sides. These serve as your handles to remove the brownies from the pan in 1 piece, so make sure that there is enough of the overhang for you to have a solid grip. Grease the parchment or foil well.
Stir in the vanilla into the cooled fudge mixture to loosen it up. Add the eggs into the mixture 1 at a time, adding the second egg after the first egg is fully incorporated. The batter should look shiny and well blended. Add in your flour and stir it until it's fully incorporated. Once it looks fully blended, beat the batter vigorously for at least 45 strokes. This'll not only get out any pent up stress, but it will make the brownies chewy. Fold in your chocolate chips. Spread the very thick and fudgy brownie batter evenly in the lined pan with an offset spatula or your greased hands.
Pop the brownies in the oven and bake until they get a nice crust and your house smells like brownies, 30 to 35 minutes. Let them cool completely on a rack or a dishtowel on your counter.
While the brownies are cooling make the buttercream and ganache.
For the buttercream: Mix your peanut butter and butter together in a stand mixer until they are totally blended. Turn your mixer down and slowly add your powdered sugar and fine sea salt. Stop the mixer and scrape the sides and bottom of the bowl. Turn your mixer back to medium, add your milk and vanilla and keep mixing until it's fully blended. Dollop the peanut butter buttercream in heaping spoonfuls on top of the cooled brownies. Evenly spread it with the back of a butter knife the over the surface. Scatter the peanuts evenly over the buttercream, pressing into the buttercream so that the ganache has something to hold on to and the peanuts are all covered.
For the ganache: Melt the chocolate chips and butter together in a small saucepan over low heat, stirring constantly. Allow the ganache to cool down slightly for 10 minutes or so, then pour it evenly over the peanut butter buttercream layer. Smooth the ganache out with the back of a butter knife, making sure to cover the buttercream and peanuts completely. Chill the brownies in the refrigerator until the toppings are set, 1 1/2 hours or so.
Remove these delicious guys from the refrigerator. Lift up the ends of the foil liner and place the Fudgy Salty Chocolate Peanut Butter Brownies on a cutting board. Cut into squares.