For the crust: Preheat the oven to 350 degrees F. Line a 24-cup muffin tin with cupcake liners.
Pulse the graham crackers in a food processor until fine crumbs form. Add the butter and sugar, then pulse until well combined. Distribute the crumbs among the prepared cups, about 2 tablespoons in each, and press to firm them up.
For the filling: Beat the cream cheese in an electric mixer fitted with the paddle attachment until smooth. Mix in the sugar and eggs. Add the vanilla and 3 tablespoons of the salted caramel and mix again. Distribute the batter among the muffin cups, about 3 tablespoons per cup. Tap the tin on the counter to distribute the batter evenly.
Bake, watching to make sure they don't burn, until set in the middle, 15 to 17 minutes. Cool on a wire rack, then chill for 2 hours.
For the ganache: Place the chopped chocolate in a bowl and set aside. Heat the cream in a saucepan until warm and bubbles begin to form around the edges, 1 to 2 minutes. Pour over the chocolate and allow to sit for 2 minutes. Mix until smooth, then set aside to cool slightly.
Place about 1 tablespoon ganache on top of each cheesecake. Sprinkle the top with the pecan pieces and mini chocolate chips. Drizzle with the remaining 1/4 cup plus 1 tablespoon caramel and freeze, uncovered, for 1 hour. Transfer to an airtight freezer container and freeze for up to 3 months.
Allow to thaw at room temperature for 30 minutes before serving.