Preheat oven to 350°F (175°C). Lightly grease the bottom of a 9x13-inch baking dish.
In a large bowl, combine flour, softened butter, ¾ cup chopped pecans, granulated sugar, and salt. Mix with a fork or your hands until the mixture looks like coarse, crumbly dough that holds together when pressed.
Tip the crumbs into the prepared dish and press them into an even layer across the bottom, using the flat base of a measuring cup for a smooth surface.
Bake for 18 to 20 minutes, until the edges are lightly golden. Set the dish on a rack and let the crust cool completely, at least 30 minutes.
Put the softened cream cheese in a medium bowl and beat it on its own for about a minute until smooth. Add the powdered sugar and beat again until fully combined with no white streaks.
Beat in the vanilla extract and the fresh lemon zest. Fold in 1 cup of the thawed whipped topping with a spatula, gently, until the mixture is light and even. Spread this layer over the cooled crust in an even sheet, all the way to the edges.
In a separate bowl, whisk together both packages of instant lemon pudding mix and the 3 cups of cold milk. Whisk steadily for about 2 minutes, until the mixture starts to thicken. Whisk in the lemon extract now if you are using it.
Let the pudding stand for 5 minutes to firm up to a spreadable, custardy set. Spread the pudding gently over the cream cheese layer, being careful not to pull the layer below up into it.
Spread the remaining whipped topping (about 2 cups) evenly over the pudding layer. Scatter the reserved ¼ cup of chopped pecans over the top. Add lemon slices or a little extra zest for color.
Cover the dish loosely and refrigerate for at least 4 hours, or overnight for the cleanest slices. Cut into squares with a sharp knife, wiping the blade between cuts, and serve cold.