Bake the Cakes: Preheat oven to 350°F. Grease, flour, and line two 9 inch cake pans with parchment. Whisk flour, cocoa, salt, baking soda, and powder in a bowl. Combine coffee and milk in a cup.
In a stand mixer, cream butter and sugar for 5 mins until fluffy. Beat in eggs one at a time. On low, alternately add dry ingredients and coffee milk mixture in 3 parts, starting and ending with dry ingredients. Beat on medium 2 mins.
Divide batter between pans. Bake 23-28 mins, until a toothpick comes out clean. Cool in pans 10 mins, then invert onto wire racks to cool completely.
Make the Filling: In a saucepan, whisk flour into milk until smooth. Cook over medium heat, whisking constantly, until very thick (like pudding). Remove from heat, stir in vanilla, and transfer to a dish. Press plastic wrap on surface and cool to room temp.
In a clean mixer bowl, beat butter and sugar for 4-5 mins until pale. With mixer on medium low, add spoonfuls of the cooled flour paste. Once added, beat on high for 3-4 mins until light, fluffy, and like whipped cream.
Make the Ganache: Place chocolate chips in a heatproof bowl. Heat cream in a saucepan until simmering. Pour hot cream over chocolate, let sit 3 mins, then whisk until smooth. Let cool 5-10 mins to thicken slightly.
Assemble: Place one cake layer on a plate. Spread all filling evenly on top. Top with second cake layer. Pour slightly cooled ganache over the center, guiding it over edges with an offset spatula to cover completely. Let set 30+ mins before slicing.