Prepare the cupcakes according to package directions. Remove from oven and allow to cool.
In a saucepan, add the milk and vanilla. Bring to a simmer.
In a separate mixing bowl, whisk together the eggs, flour and sugar. Temper the eggs by whisking in 1/4 of the hot milk mixture. Then pour the tempered eggs into the remainder of the milk.
Bring the mixture up to a simmer, stirring constantly until thickened. Set aside and allow to cool.
In another large mixing bowl, add the powdered sugar, cocoa and salt. Add the butter and beat in with an electric mixer. Pour in the cream. Mix on low speed until moistened, then increase speed and whip until fluffy.
Pour the cooled custard into a piping back. Fit another piping back with your choice of frosting tip, and spoon in chocolate frosting.
Use a long, cylindrical implement (finger or end of a mixing spoon, etc) to poke large holes in the center of the cupcake. Snip off the corner of the custard back and squeeze filling in to each cupcake (you will likely have filling left over). Top with chocolate frosting.