In medium bowl, sift cocoa with flour, salt, baking soda and baking powder, set aside. In measuring cup, mix coffee and milk together. Set aside.
In mixer, beat butter and sugar for about 5 minutes until smooth. Beat in eggs one at a time. Slowly add in dry ingredients alternating with the coffee/milk blend (about 3 additions of each).
Pour cake batter into two prepared pans (two 9inch cake pans lined with parchment paper and then greased and floured). Bake in a 350 degree oven for about 25 minutes. Remove and allow to cool about 10 minutes before removing from pans. Cool completely before frosting.
For frosting: in food processor, pulse dark chocolate until small bits (not powder). Set aside. In mixer, beat butter, powdered sugar and milk (slowly add the milk, you may not need it all) for 3-5 minutes, until smooth and creamy. Add in extract and food coloring gel. Mix until fully blended. Add more milk if necessary to desired consistency. Fold in chopped dark chocolate or chocolate chips.
Frost first layer of cake, then top it with second layer. Completely frost sides and top of cake.
For the ganache, heat 3/4 cup heavy cream in saucepan. Bring just to a boil and remove from heat. Place chocolate chips in a bowl then slowly add in hot cream and extract. Stir until smooth and completely combined. Allow ganache to cool then pour over chocolate cake.