Preheat oven to 350F. Fill the wells of a jumbo cupcake pan with liners. If you are halving the recipe, fill the empty wells halfway with water.
Fill a medium saucepan with a couple of inches of water. Bring the water to a gentle simmer over medium low heat. Add butter and chocolate to a medium heatproof bowl and set it over the saucepan of water. Heat until the chocolate and butter are melted, whisking occasionally. Add the cocoa to the melted chocolate and whisk until smooth. Set the bowl aside and let cool until just warm to the touch.
In a small bowl, whisk together the flour, baking soda, baking power, and salt.
In a large bowl, whisk together the eggs, then add in the brown sugar and vanilla. Pour in the cooled chocolate and whisk until smooth. Whisk in 1/3 of the flour mixture, then 1/2 of the sour cream, another 1/3 of the flour, the remaining sour cream, and the remaining flour. Batter should be thick and smooth.
Add 1/2 cup of batter to each cupcake liner. Bake the cupcakes for 18-19 minutes. A toothpick will still be a little wet if you put it the middle of the cupcakes. Let the cupcakes cool in the pan for a few minutes then carefully move them to a cooling rack.
Once the cupcakes have cooled for about 15 minutes on the rack, remove a 2 inch section of cupcake top from each. If needed, scoop out some of the middle so you have enough room for 2 tbsp of filling. Add 1 tbsp of ganache and 1 tbsp of strawberry compote to each cupcake. Replace the tops. Then spread another tablespoon or two of ganache over the top of each cupcake. Let the cupcakes cool completely to room temperature.