Step 1: Prepare the Oven and Pan: Preheat the oven to 325°F. Line a standard 12-cup muffin tin with paper liners.
Step 2: Make the Cinnamon Graham Crust: In a food processor, pulse the graham crackers until they form fine, even crumbs. Add the sugar, salt, and melted butter and pulse until the mixture is evenly moistened. The texture should resemble wet sand. If you do not have a food processor, place the crackers in a sealed bag and crush them with a rolling pin before mixing with the remaining crust ingredients.
Step 3: Form and Pre-Bake the Crusts: Spoon about 1½ tablespoons of crumb mixture into each liner. Press firmly into an even layer using the bottom of a small glass, measuring cup, or tart tamper. Bake the crusts for 5 minutes, then remove from the oven and allow them to cool slightly. Leave the oven on.
Step 4: Melt the Chocolate and Bloom the Spices: Place the chopped chocolate in a heatproof bowl. Microwave in 20-second intervals, stirring after each interval until smooth and fully melted. Alternatively, melt the chocolate using a double boiler. Stir the cinnamon, cloves (if using), cayenne, and kosher salt into the warm melted chocolate. Set aside to cool slightly while you prepare the cheesecake batter.
Step 5: Beat the Cream Cheese: In a large bowl, beat the cream cheese with an electric mixer on medium speed for 2-3 minutes, until completely smooth and creamy with no lumps. Scrape down the sides and bottom of the bowl as needed.
Step 6: Add the Sugars: Add the granulated sugar and brown sugar. Beat for 1-2 minutes, until fully incorporated and the mixture looks light and creamy.
Step 7: Mix in Sour Cream and Vanilla: Add the sour cream and vanilla extract. Mix on low speed until smooth and well combined, about 30 seconds.
Step 8: Add the Eggs: Add the eggs one at a time, mixing on low speed after each addition just until incorporated. Avoid overmixing at this stage, as too much air in the batter can cause cheesecakes to crack. Scrape the bowl and give the batter a final gentle stir to ensure everything is evenly combined.
Step 9: Mix in the Melted Chocolate: Pour the slightly cooled chocolate mixture into the batter. Mix on low speed just until the batter is evenly combined and uniformly chocolate-colored. Do not overmix.
Step 10: Fill the Muffin Cups: Divide the cheesecake batter evenly among the 12 liners, filling each about ¾ full. Gently tap the pan on the counter 2-3 times to release any air bubbles.
Step 11: Bake: Bake for 17-22 minutes. The cheesecakes are done when the edges are set, but the centers still jiggle slightly when the pan is gently shaken. The centers should not look wet or liquid.
Step 12: Cool, Chill & Serve: Remove the pan from the oven and allow the cheesecakes to cool completely at room temperature on a wire rack, about 1 hour. Once cooled, cover the pan with plastic wrap or transfer the cheesecakes to an airtight container. Refrigerate for at least 4 hours, preferably overnight, to allow the texture to set fully. Before serving, garnish with whipped cream and chocolate shavings, if desired.