Preheat oven to 325°F (170°C). Spray a 12-cup muffin pan with cooking spray.
In the top of a double boiler, combine chocolate, butter, and ¼ cup (64 grams) peanut butter. Cook over simmering water, stirring occasionally, until melted and smooth. Remove from heat. Let cool for 10 minutes.
In a large bowl, beat eggs with a mixer at medium speed. Add sugar and salt in a slow, steady stream, beating until pale yellow, about 2 minutes. Fold in chocolate mixture and vanilla until combined. Fold in cocoa.
Press 2 tablespoons (38 grams) Cookie Crust into bottoms and up sides of prepared muffin wells. Divide batter among prepared crusts (about 3 tablespoons or 50 grams each).
Bake until tops are dry and a wooden pick inserted in center comes out with a few moist crumbs, 15 to 20 minutes. Let cool in pan for 10 minutes. Remove from pan, and let cool completely on a wire rack. (Centers will fall as they cool)
In a small microwave-safe bowl, heat milk and remaining ½ cup (128 grams) peanut butter on high in 10-second intervals, stirring between each, until peanut butter is melted and mixture is smooth. Drizzle glaze onto cooled cookie cups.