|Prepare 3 muffin tins with cupcake liners. Chop one chocolate bar into small pieces (1/8- to 1/4-inch) and set aside; these will go into the cheesecake batter. Chop the second chocolate bar into larger chunks and slivers (1/2-inch); these will be used to garnish the cheesecake tops after baking.
Stir together graham crackers, butter, sugar and salt in a bowl. Press a heaping tablespoon of crumb mixture firmly into the bottom of each cupcake liner. Can be prepared in advance and chilled for up to two hours.
Preheat oven to 350°F.
Beat together cream cheese, sugar, flour and zests with an electric mixer until smooth. Add eggs and yolks, one at a time, allowing them to blend into the mixture and scraping down the bowl between additions. Add vanilla, beating on low speed until incorporated. Do not overmix or you risk adding in too much air. Add chocolate-covered pretzel pieces and smaller chocolate chunks to the batter and gently fold in, using a spatula or wooden spoon.
Add 1/4 cup of cheesecake batter to each cupcake liner on top of the crust layer. After each cup is filled, tap pan on the counter to allow any air bubbles to work out.
Bake for 15 to 20 minutes. The cream cheese should puff up. Bake until cakes are mostly firm (centers may wobble slightly when pan is gently shaken) and the surface looks dull, not shiny. Cool on a rack for 10 minutes before removing individual cakes. Allow to cool further on wire rack. When completely cool, refrigerate for 4 hours or overnight before serving.
Before serving, garnish each mini cheesecake with a few chocolate chunks.