Preheat the oven to 350°F and line cupcake pan with paper cases. Set aside.
Place chocolate and cocoa powder in a small heat proof bowl. Add the boiling water and whisk until smooth. Set aside to cool slightly.
In a large bowl, sift together the flours, baking soda, and salt. Whisk and set aside.
Beat butter on a medium- high speed for about a minute, or until creamy. Add brown sugar and beat on a high speed until fluffy, about 3 minutes. Scrape the bowl down.
With the mixer on a medium- high speed. Carefully add the eggs one at a time, mixing until combined after each addition. Scrape the bowl down.
Add the sour cream and vanilla and beat on a medium speed until combined, about 10 seconds. Scrape the bowl down.
Add a third of the dry ingredients and beat on low until just combined. With the mixer running, add half of the chocolate mixture and beat until just combined.
Add another third of the dry ingredients and beat on low until just combined. With the mixer running, add the remaining chocolate mixture and beat until just combined.
Add the last of the dry ingredients and beat until just combined. Do not over beat. Scrape the bowl down and fold gently to combine.
Use a large cookie scoop (about 1/4 cup) to evenly dispense the batter into the cupcake pans. Bake for 15- 18 minutes. Cool in the pans for 5- 10 minutes before transferring to a cooling rack. Cool completely before assembling.