Heat the oven to 325°F. Lightly grease a 9-inch springform pan. Add a parchment round to the bottom if desired. Set one oven rack in the center and another rack below it.
Make the crust. Stir the graham cracker crumbs, chopped pecans, sugar, and salt together. Add the melted butter and mix until evenly moistened.
Press the crumb mixture across the bottom and about 1 inch up the sides of the pan. Bake for 10 minutes. Set on a wire rack while making the filling.
Beat the softened cream cheese on low to medium-low speed until smooth. Scrape the bowl. Add the brown sugar and mix until combined.
Mix in the sour cream, vanilla, lemon juice, cinnamon, and salt on low speed. Scrape the bowl again.
Add the eggs one at a time, mixing on low only until each egg disappears into the batter. Fold the batter a few times by hand.
Pour the filling over the warm crust and smooth the top. Tap the pan gently on the counter two or three times and pop any large bubbles.
Place the cheesecake on the center oven rack. Put a metal roasting pan on the rack below it and carefully add about 1 inch of boiling water.
Bake for 65 to 80 minutes. The outer 2 to 3 inches should be set, while the center should wobble gently as one piece.
Turn off the oven, crack the door open about 1 inch, and leave the cheesecake inside for 60 minutes.
Transfer the cheesecake to a wire rack and cool for 1 hour. Cover and refrigerate for at least 6 hours or overnight.
Make the topping. Melt the butter in a medium saucepan over medium-low heat. Stir in the brown sugar, maple syrup, corn syrup, cream, and salt.
Bring the mixture to a gentle simmer and cook for 2 minutes, stirring often. Remove from the heat and stir in the vanilla and toasted pecans.
Cool the topping for 20 to 30 minutes, until thickened but still spoonable.
Remove the springform ring from the cold cheesecake. Spoon the pecan topping over the top. Finish with flaky salt if desired. Rest at room temperature for 15 to 20 minutes before slicing.