Heat the oven to 350°F and arrange a rack in middle. Butter a 2-quart baking dish then line with parchment paper or aluminum foil, leaving a few inches of overhang on each side. Combine 3/4 cup of the pecans with the 1/2 cup of sugar, and 1 teaspoon of the kosher salt in a food processor. Pulse until the nuts are a coarse meal. Add the flour and process until it's a fine meal and evenly mixed. Cut 8 tablespoons of the butter into small cubes, add it, and pulse until the mixture comes together in a clump. Press the mixture evenly into the prepared baking dish, using the back of a measuring cup to even the shortbread out in the pan. Place the shortbread in the freezer for 10 minutes before baking. Bake the crust until lightly golden and set throughut, about 25 to 30 minutes. Remove from the oven and let cool at least 20 minutes before continuing. Meanwhile, make the filling.(You can make the bars through this step up to 3 days ahead. Let cool completely then wrap securely and refrigerate.)
Make The Cheesecake Batter:
Combine the cream cheese and 1 cup of the sugar in a bowl of a food processor and process until the mixture is smooth. Scrape down the sides of the processor then add the eggs and the yolk one at a time. Add the vanilla extract and 1/2 teaspoon of the kosher salt and pulse until blended.
Pour the mixture over the baked shortbread and bake until a toothpick or cake tester inserted into the cake comes out clean and the center of the cheesecake is just set (it will look like custard), about 40 minutes. Turn off the oven, leave the door slightly ajar, and let the cheesecake cool for 15 minutes.
Remove cheesecake from the oven and set on a rack to cool. Coat a butter knife with oil or butter (or run it under very hot water) and then run it around the perimeter of the cheesecake. Let the cheesecake cool completely, about 1 hour. (You can make the bars through this step up to 3 days ahead. Let cool completely then wrap securely and refrigerate. Let sit at room temperature at least 15 minutes before adding the caramel sauce.)
Make The Caramel Sauce:
Once the cheesecake is cool, make the caramel. Stir together the remaining 1 cup of the sugar and water in a small saucepan until the sugar is completely moistened. Brush the insides of the saucepan with a wet pastry brush to remove any sugar granules then place the pan over medium-high heat and bring to a boil.
Without stirring but swirling the pan occasionally, let the sugar boil until it turns amber in color, about 5 minutes. Give the pan a few good swirls to make sure it’s evenly cooking, remove from heat, and carefully add the whiskey. (The caramel will seize but just keep swirling the pan until the alcohol smell is cooked off.) Immediately add the remaining 2 tablespoons of butter and cream, and swirl until the caramel is smooth and uniform in color. Set aside to cool to room temperature, at least out 15 minutes.(You can make the bars through this step up to 1 day ahead. Let cool completely then wrap securely and refrigerate. Let sit at room temperature at least 15 minutes before serving.)
Assemble The Cheesecake Bars:
Pour the lukewarm caramel over the cooled cheesecake, then place in the refrigerator to chill for a minimum of 2 hours. When ready to serve, cut into slabs or squares using a sharp knife dipped in hot water. Garnish with sea salt and serve.