Ride height

So there's 2" between the bump stop and the upper control arm? That would suggest the car is actually lowered a bit.

Can you take a picture of how you're measuring the ride height? Would also be helpful to see the angles that the control arms are sitting at to get a better idea of where you're at. I don't actually ever worry about the factory setting as all of my cars are lowered, I just set them where I want them and do the alignment.