Make the crust: Preheat the oven to 325˚. Melt 6 tablespoons butter. Pulse the graham crackers in a food processor until finely ground. Add 3 tablespoons sugar and 1/4 teaspoon salt and pulse to combine. Drizzle in the melted butter and pulse to make moist crumbs. Press the crumbs on the bottom and up the sides of a 9-inch pie plate. Bake until toasted, 10 to 12 minutes.
Make the brownie layer: Increase the oven temperature to 350˚. Combine the remaining 6 tablespoons butter and the chocolate in a heatproof bowl set over a saucepan of simmering water (do not let the bowl touch the water); cook, stirring, until melted, about 3 minutes. Remove the bowl from the pan. Whisk in the remaining 1/2 cup sugar and 1/4 teaspoon salt, then the egg yolks and vanilla. Whisk in the flour until just combined. Spread the batter evenly over the crust. Bake until just set on top, about 20 minutes.
Meanwhile, make the pumpkin layer: Whisk the pumpkin puree and heavy cream in a medium bowl until smooth. Whisk in the egg and vanilla. Stir in the sugar, flour, pumpkin pie spice and salt until smooth. Pour over the hot brownie layer and spread evenly with a rubber spatula. Return to the oven and bake until the pumpkin layer is set, 10 to 15 minutes (cover the edges with foil if the crust is getting too dark). Transfer to a rack and let cool completely in the pan, then refrigerate until cold, at least 2 hours. Serve with whipped cream.