Preheat oven to 350 degrees (F). Line two large baking sheets with parchment paper and set aside. 

In a large bowl whisk together the flour, baking powder, baking soda, cinnamon, and salt. Set aside. 

In the bowl of a stand mixer fitted with the paddle attachment, or in a large bowl using a handheld electric mixer, beat the peanut butter and butter until smooth. 

Gradually add in both sugars, one at a time, and beat until well combined, about 2 minutes. 

On low speed, add in the eggs and egg yolk, one at a time, beating well after each addition, and scraping the sides and bottom of the bowl as needed. Beat in the vanilla and bourbon. 

Gradually add in the dry ingredients, beating on low speed until just combined. Turn the mixer off. 

Using a rubber spatula, fold in the chocolate chips and chocolate chunks.

Using a large cookie scoop, scoop out 1/4 cup portions of the cookie dough and roll it into balls. Place the balls on the prepared baking sheets, leaving at least 2-inches between each cookie for spreading.

Gently press pretzels pieces down on top of each cookie ball, slightly flattening the ball. This will help them spread evenly in the oven. 

Bake, one tray at a time, for 14 to 16 minutes, or until golden brown and set. Repeat with all cookie dough. 

When the cookies come out of the oven, press a few extra chocolate chips and/or chocolate chunks on top while they're still warm, and sprinkle with sea salt, if desired. Serve warm or cooled!