1. Make crust: Preheat oven to 375°F; butter a 10-inch springform pan. Wrap outside bottom of pan with 2 layers of heavy-duty foil. Pulse graham crackers, pecans, sugar and salt in a food processor until fine crumbs form. Pulse in butter. Press mixture over bottom and 1 inch up sides of pan. Bake until lightly browned around edges, 12 to 14 minutes. Allow to cool on a wire rack. Reduce oven temperature to 325°F. Set springform pan in center of a large roasting pan. Bring a kettle of water to a boil.
2. Make filling: Using an electric mixer on medium speed, beat cream cheese, dulce de leche, flour, brown sugar and salt until smooth. Add eggs one at a time, beating well after each. Scrape down bowl and beaters as necessary. Beat in vanilla.
3. Pour filling into crust. Carefully add boiling water to roasting pan to a depth of 1 inch. Bake until cheesecake is firm around edges and just set in the center, about 1 hour and 40 minutes.
4. Make topping: Mix sour cream, sugar and vanilla in a small bowl. Remove roasting pan from oven and increase temperature to 400°F. Spread topping over surface of cheesecake and drop teaspoons of dulce de leche over the top. Use a small, sharp knife to make decorative swirls. Return to oven and cook until top is set, about 10 minutes. Remove cake from water bath, peel off foil and transfer cake to a wire rack. Run a sharp knife around cake edge to loosen, then let cool for 30 minutes. Refrigerate uncovered until completely cool, then cover tightly with plastic wrap and refrigerate for at least 12 hours or overnight. To serve, loosen sides of pan and transfer cake to a serving plate. Cut wedges with a long thin knife, dipped in hot water and wiped clean between slices.