In a bowl, whisk together flour, baking soda, salt and sugars. Set aside.
In another bowl, combine the chocolate, coffee and cocoa powder. Boil the water and pour over the chocolate mixture.Let it sit for one minute and whisk together until all the chocolate is melted and it forms a smooth and homogenous mixture. Cool.
Whisk together the yogurt + vinegar mixture, oil, eggs and vanilla. Add to the chocolate mixture and whisk together. Add half of the dry ingredients to the chocolate mixture, mix until just combined. Add the rest of the flour mixture until just absorbed and there are no lumps.
Scoop over cupcake tins and bake at 350F for 20-25mins, or until done.