Preheat oven to 350 degrees F. Line a 9x13 baking pan with aluminum foil and spray with nonstick cooking spray.
In a large pot melt the butter over very low heat, then add in the semi-sweet chocolate chips. Whisk continuously until the chocolate chips are completely melted and smooth, then remove the pot from the heat.
Whisk in the cocoa powder, sugar, coffee granules, vanilla extract, and salt, then whisk in the eggs, one at a time, until the mixture is smooth. Add in the flour, a little at a time, stirring until no white streaks remain. Fold in the chopped peanut butter cups and milk chocolate chips and mix well.
Pour the batter into the prepared baking pan (the mixture will be VERY thick at this point), spread evenly, and bake in the preheated oven for 35-40 minutes or until a toothpick inserted in the middle comes out mostly clean, with just some melted chocolate remaining on the toothpick. Top immediately with peanut butter chips, then place the pan on a wire rack until cool enough to refrigerate until slicing ( refrigerating makes slicing easier) .