Preheat the oven to 350 degrees. Grease and flour a 9 x 13 inch baking pan.

In a large bowl, whisk together the cocoa powder, sugar, flour, salt, soda, and baking powder. (Note: If your cocoa powder is clumpy, you may need to sift it before whisking in).

Make a hole in the center of the dry ingredients, then pour in the water, oil, vinegar, and vanilla.

Mix all the ingredients together until smooth. Pour in the prepared baking pan and bake for 30-35 minutes, or until toothpick inserted in the center comes out clean. Cool.

Whisk together flour and milk in a sauce pan. Heat the mixture over medium heat, whisking often, until bubbly and thickened. This will take several minutes, but once it starts to thicken it will go quick, so keep an eye on it, and keep whisking. The mixture should be about the consistency of mayonnaise. Remove from heat and allow to cool to warm.

Meanwhile, in an electric mixer, beat together the sugar, shortening, vanilla and salt. Add cooked mixture to shortening mixture and beat on medium high speed until thick and fluffy, about 5-7 minutes. Spread evenly over the cooled cake.

Place the chocolate chips in a bowl. Heat cream until just barely simmering, then pour over the chocolate chips. Whisk until chips are melted. Cool until ganache is still pourable, but slightly thickened. Pour over the filling and gently spread to the edges. Allow the ganache to set up completely before slicing and serving.