Line a 13x9 inch baking pan with foil, letting the ends extend up the sides. Set aside 1-1/2 cups pretzels for topping. Pulse remaining pretzels in a food processor until they're fine crumbs. In a large bowl, mix butter, peanut butter, confectioners' sugar, and pretzel crumbs.
Press into prepared pan. In a microwave, melt chocolate chips and shortening; stir until smooth. Layer over the peanut butter mixture. Break reserved pretzels and sprinkle over top; press down gently. Refrigerate, covered, until set, about 1 hour. Lifting with foil, remove from pan. Cut into 48 bars.