For the cake, preheat the oven to 350 degrees F.
Line 3, 6-inch circle cake pans with parchment and spray with cooking spray.
In a medium bowl, sift the flour, salt, baking powder, and cocoa.
Melt the chopped chocolate and set it aside to cool until it's warm to touch (not hot).
In a large bowl, whisk the sugar and oil until combined.
Add the melted and slightly cooled chocolate.
Add the eggs and yolks one at a time, and whisk until just combined.
Add the vanilla and sour cream (or Greek-style yogurand mix until combined.
Add the dry ingredients. Mix until just combined.
Mix the warm water and the espresso powder. Add the coffee mixture to the batter. Mix until just combined.
Fill the prepared cake pans evenly with the batter.
Bake for 20 to 25 minutes until a toothpick inserted in the center of the cake comes out clean.
Allow the cakes to cool in the cake pan on a cooling rack for about 15 minutes.
After 15 minutes, turn the cakes out of the pans, and allow them to cool completely on a cooling rack.
While the cakes cool, make the peanut butter frosting. In the bowl of a stand mixer fitted with a paddle attachment, beat the butter and peanut butter until well-combined and light and fluffy.
Then add the vanilla and salt. Mix until combined.
Next add the confectioners' sugar. Mix until combined.
Add the milk and mix until light and fluffy.
Before filling the cakes, using a serrated, level each of the cakes.
Stack the cakes, spreading about 1/4 cup of frosting between each layer and sprinkling each layer with chopped peanut butter cups.Using a large tip, pipe a border on the edge of the cake layer.
Repeat this process with the next layer of cake. Once filled and stacked, use the tip of an off-set spatula to flatten the exposed frosting so that it is flush with the edges of the cake.
Spread an additional 1/4 cup of frosting on top of the cake, but do not add peanut butter cups to the top layer. You want a smooth peanut butter frosting for the ganache to sit on top of the cake.
Chill the cake for about 15 minutes in the refrigerator.
While the cake chills, make the ganache by warming the cream until simmering.
Pour it over the chopped chocolate and add the vanilla.
Mix until smooth and creamy.
Allow the ganache to cool and thicken for about 5 to 10 minutes.
Once cooled, remove the cake from the refrigerator. Pour the chocolate over the top of the cake. Use an offset spatula, smooth the chocolate on top of the cake. Place the cake in the fridge to chill for about 10 minutes.
Once the ganache has chilled a bit, pipe dollops of peanut butter frosting on top of the cake. Top each dollop with a mini-peanut butter cup.