Make the cake: Preheat the oven to 325°. Spray the bottom and sides of a pudding pan or Bundt pan with nonstick baking spray.
In a medium saucepot, bring the molasses, coffee and water to a boil. Remove from the heat and carefully whisk in the baking soda. Set aside to cool slightly, about 15 to 20 minutes.
In a medium bowl, whisk together the flour, cocoa powder, baking powder, ground ginger, cinnamon, cardamom, cloves, salt and black pepper. Set aside.
In a large bowl, whisk together the eggs, brown sugar, granulated sugar, fresh ginger, lemon zest and grapeseed oil. Gradually whisk in the reserved molasses mixture and flour mixture a third at a time, alternating until the mixture is just combined.
Pour the batter into the prepared pan and place in the oven. Bake until a tester comes out clean, about 45 minutes to 1 hour. Place the cake on a cooling rack and let cool in the baking pan for 5 minutes. Carefully turn the cake out onto a cooling rack and cool completely.
Make the cognac glaze: In a small bowl, whisk together the confectioners' sugar, cognac, water, vanilla-bean seeds and a pinch of salt until smooth. Pour the glaze over the cooled cake and serve.