Sounds like there is still air in the calipers, but be aware there are four different calipers for each side. There's an 80mm piston and an 88mm piston. Using the larger one means it needs more fluid and the pedal will go down further.
There's also the standard caliper and a low-drag caliper that releases a little more for better fuel mileage. You need to be aware of that not for the low pedal, but because there is a 32 page service bulletin about correcting / avoiding a brake pull when hot on the heaviest trucks including the diesels. Of particular importance, the two brake rotors MUST be the same thickness and the same speed of cut to prevent them from heating up at different rates. I was involved with three of these brake pulls. One had rotors that were only.007 inches different thickness. That's the thickness of two sheets of paper on a rotor that's 1 1/4 inches thick! It had no brake pull whatsoever until they got hot from repeated stops from highway speed. At the eighth stop, it just about tugged the steering wheel out of your hand. Remachining both rotors to exactly the same thickness solved the pull.