Preheat oven to 375°F. In a mixing bowl, whisk together flour, baking soda, and salt until combined. Set aside.

Combine butter, peanut butter, 1/2 cup granulated sugar, and brown sugar in the bowl of a heavy-duty stand mixer. Beat on medium-high until light and fluffy, 3 minutes. Scrape down sides of bowl and add eggs one at a time, beating for 1 minute after each addition. Add vanilla and milk; beat on medium-high until airy and doubled in volume, about 2 minutes. Add flour mixture to wet ingredients and incorporate on low speed until just combined, about 1 minute.

Place remaining 1/4 cup granulated sugar in a small bowl. Portion dough into 1 1/2-inch balls and roll in granulated sugar. Place sugar coated dough balls 2 inches apart on a parchment paper-lined baking sheet.

Bake for 8 minutes, remove from oven, use the round side of a rounded 1/2 tablespoon measuring spoon to press a crater into the center of each puffed dough ball (the dough will crack and create a rounded crater around the measuring spoon). Return to the oven and bake until light golden brown, 3-5 minutes. Transfer to wire racks to cool completely, about 30 minutes.

Melt chocolate and shortening together in a microwave-safe bowl by microwaving in 30 second intervals on 30% power, stirring between each interval, until completely melted. Transfer melted chocolate to a pastry bag fitted with a small round piping tip. On one cookie, pipe 2 sets of 4 lines originating in the crater and running parallel to each other on either side of the cookie for the illusion of spider legs. Repeat with remaining cookies. Place one chocolate truffle in each crater. Use remaining melted chocolate in piping bag to adhere the candy eyeballs onto the faces of each truffle.