Half a gallon of water is 20% of your batch size there, that would easily explain the gravity difference. Next time, just boil it longer if you overshoot the volume, or like was mentioned above use Promash to help you.
My BYO article on the Dogfish 90 calles for the 32 degree step at the end, I think it's to drop the yeast out for clarity purposes. I would definately skip this step and just age it longer if you are planning on carbonating naturally, because you're right, the yeast should drop to the bottom and go into hibernation at that tempurature.
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