In a small microwavable-safe bowl add chocolate and butter, and heat for 30 seconds, stir and heat again for 30 seconds. Stir until chocolate is completely melted. If needed, heat once more for 15 seconds. Make sure not to overheat the chocolate.
In another small mixing bowl sift together flour, baking powder, and salt.
In a medium mixing bowl with electric beaters or stand mixer beat eggs, brown sugar, and vanilla on high speed until light and fluffy; about 3-4 minutes.
Reduce the mixing speed to low and add in melted chocolate while continuing to beat together until well combined. Add flour mixture and beat until just combined. Once combined stir in the chocolate chunks.
Line a baking pan with parchment paper and add a heaping tablespoon of dough, I used a small cookie dough scoop. Bake for 10-12 minutes, larger cookies 12-15 minutes or until cookies are shiny & crackly yet still soft and chewy in the center. Cool the cookies on baking sheets for 5-10 minutes, then transfer to a wire rack to cool completely.
Filling
Add milk into a small sauce pan over medium-low heat, immediately whisk in flour until no lumps are left. Cook and stir until mixture is thick cold milk into a small saucepan, like a pudding or gravy. Yes, you are making a roux for a dessert.
Remove from heat, stir in the vanilla, set it aside and let it completely cool.
Once cooled, cream together butter and sugar using an electric or stand mixer. Beat on medium-high speed, until light and fluffy, about 7-8 minutes.
Add in the cooled milk mixture and beat again until mixture is creamy and looks like whipped cream.
Ganache
In a small saucepan add the whipping cream and bring to a boil, remove from heat and add in chocolate chips. Do not mix or stir them in, let the chocolate sit for 5 minutes. Stir until smooth. Let it cool for about 15 minutes while filling the cookies.
Assembly
In a frosting piping bag or Ziploc with the corner snipped off and add the filling into the bag.
Pipe some frosting on top of one cookie, add filling, and top with another cookie. You can also just spread a thick layer of frosting, no need for a piping bag. Keep it simple, just like a sandwich.
Repeat this step with remaining cookies and frosting.
Spoon slightly cooled ganache over each cookie. Place in fridge until the ganache is set, and then serve.