Line a cupcake pan with paper liners, and preheat the oven to 325°F.
In a small saucepan, combine 3.5 ounces bittersweet chocolate and 1 cup water, and heat over low, stirring until it melts and is smooth. Set aside to cool.
In a stand mixer, cream 4 ounces butter and 1 1/4 cup dark brown sugar until pale and creamy.
Add 3 large large eggs, one at a time, until just combined.
Combine 1 1/2 cup self rising flour, 1/2 cup all-purpose flour, and 1/4 cup unsweetened cocoa powder in a bowl.
Add the flour mixture gradually until just combined.
Add the melted chocolate and stir.
Divide batter evenly among the cupcake liners, and bake for 20 minutes.
Set aside to cool and frost.
Notes
They should spring back when touched lightly, and a skewer should come out clean.