Heat milk until hot and bubbly at the edges but not boiling.
While the milk it heating, whisk together sugar, flour, and salt in a small bowl.
In a medium bowl, whisk together egg yolks.
Gradually add the flour mixture to the egg yolks, whisking until incorporated before the next addition.
Stream milk into egg yolk mixture, whisking as you go (otherwise you will end up with scrambled eggs if you add it too quickly or all at once).
Once all of the milk is incorporated, return mixture to saucepan.
Cook, whisking continually, until it bubbles when you stop whisking it, about 4-5 minutes.
Remove from heat, and stir in vanilla extract.
Place pastry cream in a dish, and cover with plastic wrap. Press plastic wrap to the pastry cream (otherwise you’ll get a pudding skin on it).
Refrigerate at least 2 hours.
For the Cupcakes
Preheat oven to 350 F. Generously grease and flour a 12-cup muffin tin or use a cooking spray like Baker’s Joy that is a combo nonstick spray and flour.
In a medium bowl, whisk together flour, baking powder, and salt.
In the bowl of a stand mixer fitted with a paddle attachment, beat together butter, sour cream, and sugar until well-combined.
Add the eggs one at a time, beating well after each addition. Scrape down the bowl as needed.
Beat in milk and vanilla until well-combined.
Add flour mixture, and stir until just incorporated.
Divide batter between prepared muffin tins.
Bake 15-20 minutes, or until the cupcakes spring back when lightly pressed.
Cool cupcakes in the pan about 5 minutes, and then remove to wire rack to cool completely.
Once you’re ready to assemble the cupcakes, make the chocolate ganache.
For the Chocolate Ganache
Place the chocolate chips in a heat-proof bowl.
Heat the cream over low heat until just simmering. Do not boil.
Remove cream from heat and pour over chocolate chips.
Place a piece of aluminum foil over the bowl and seal.
Let the cream/chocolate chips sit for 5 minutes without stirring.
Remove the foil. Stir until the chocolate chips have melted and mixture is smooth and well-combined.
Let the ganache sit, uncovered, for 30 minutes, stirring occasionally, to set up before using.
To Assemble
Cut top off of cupcake (the domed muffin top).
Using a small (1 tablespoon) cookie scoop, scoop out a piece of cake. Discard, eat, or otherwise use the cake.
Using the cookie scoop, scoop out a scoop of pastry cream, and place it in the scooped out portion of the cupcake.
Replace top of the cupcake, gently pressing the top onto the cream.