In a large bowl, use a hand mixer on low speed to blend cream cheese, brown sugar, and granulated sugar until smooth (about 30 seconds).
Mix in flour, cinnamon, nutmeg, and ginger until well incorporated.
Add the pumpkin and vanilla, blending on low just until combined.
Add the eggs one at a time, followed by the egg yolks, mixing each time until just incorporated.
Gently tap the bowl on the counter to release any air bubbles.
Pour the filling into the cooled graham cracker crust.
Bake in the preheated oven at 325°F for 1 hour.
Once baked, turn off the oven and leave the cheesecake inside for 25-30 minutes without opening the door.
Remove the cheesecake and let it cool for 15 minutes before covering it with plastic wrap and refrigerating for at least 5 hours.
When ready to serve, slice and drizzle each piece with salted caramel sauce and optional sweetened whipped cream.
Store any leftovers in an airtight container in the refrigerator.