Add the cottage cheese and vanilla to a food processor or blender and blend. Add the cocoa powder and puree until completely smooth and blended in. This blooms the cocoa into the moisture and deepens the chocolate flavor. Set aside.
In a stand mixer, beat the softened butter, peanut butter, and both sugars together for about one minute, until combined. Scrape down the bowl.
Add the egg yolks and mix until incorporated. Add the pureed cottage cheese mixture and mix until combined.
In a separate bowl, whisk together the bread flour, instant coffee, baking soda, cornstarch, and salt.
Add the dry ingredients to the wet and gently mix just until the dough comes together and looks shaggy. Do not overmix.
Add the chocolate chunks/chips and mix until just incorporated, holding back a small handful for the tops.
Chill the dough at least 1 hour, ideally overnight.
Scoop the dough into thick mounds, about 70 grams each. Let each one form a firm ball, press a few chocolate chunks onto the top, then dip the top into granulated sugar. Place sugar side up on a lined baking sheet and gently press down into a thick disc.
Bake at 350 degrees Fahrenheit for 10 to 12 minutes, until the edges are set but the centers still look slightly underdone. Don't over bake.
Let the cookies set on the pan for a few minutes before moving them to the cooling rack. They will firm up as they cool.