Preheat oven to 325 degrees F. Line an 8×8 glass baking dish with parchment paper and spray with coconut oil spray.
Add cookies to a food processor and pulse to break down. Then add ghee and pulse to combined until a crumbly mixture is created. Place crumbled mixture in the baking dish and press down until evenly throughout the entire dish.
Add softened cream cheese to a food processor and pulse the cream cheese until smooth. Then add sugar, lemon juice, vanilla extract, and pulse to combined for 1 minute. Lastly, add eggs and blend, scraping down the sides until completely smooth. Fold in pecans.
Pour cheesecake mixture over crust and smooth throughout. Place in oven to bake for 20 minutes until the cheesecake has only slightly cooked through. While the cheesecake is baking for 20 minutes, place coconut sugar, maple syrup, molasses, vanilla extract, ghee, and salt in a small saucepan over medium heat. Whisk together until sugar has dissolved and mixture is smooth. Remove from heat and let slightly cool for about 5 minutes. While continuously whisking, add in an egg and beat until combined, then repeat with the other egg. Fold in pecans. When the cheesecake has cooked for 20 minutes, pour the pecan mixture on top of the cheesecake. Place back in the oven to bake for another 25 minutes.
After the 25 minutes, turn off the oven, crack the oven door open, and let the cheesecake rest for 1 hour in the oven. After an hour, remove cheesecake from oven, let cool completely then place in the fridge overnight until set.