Preheat the oven to 350° F. Line a 9x9 inch square pan with parchment paper.
Using a double boiler method, melt together the butter and 1 cup of the dark chocolate chips.
Stir in the coconut sugar, coffee liquor, vanilla, and instant coffee.
Beat the eggs in the bowl of a stand mixer for 1 minute, until bubbly on top, then add the chocolate mixture to the eggs.
Add the rye flour, raw cacao, baking powder, and salt. Beat until just combined.
Fold in the remaining 1/2 cup chocolate chips. Spread the mixture evenly into the prepared baking pan.
Bake for 28-30 minutes or until the brownies are just set. Transfer to a wire rack to cool.
While the brownies cool, melt the chopped dark chocolate and butter in a saucepan over medium heat until smooth. Pour half of the chocolate ganache over the brownies and smooth it out until it reaches the edges.
Swirl in the peanut butter, then place the brownies in the freezer for 15 minutes to set. Once set, pour the remaining ganache over the surface.
Allow the ganache to set slightly, then sprinkle with coarse sea salt.