First, the questions you asked:
A) Just calibrate. The standing acceleration is the steady pull of gravity, and any sudden deviation is the addition of acceleration due to hitting something. You'll also have to keep track of changes in orientation as reported by the gyroscope, so that you can disregard gravity's sudden shift to a new direction.
B) Integrate the acceleration to get the change in velocity. That squared, times mass of the phone, divided by two, is the energy (in the resting frame).
C) This one's basically unsolvable. Theoretically, if the case is flexible, the acceleration from an impact will tend to appear as a spike-like curve with a characteristic shape, so that if you have a couple of points that aren't on the peak you can estimate the whole shape. But I suspect the device is too rigid and the sampling too sparse. There's nothing you can do about this, unless the hardware will integrate acceleration for you, which I doubt (I don't know the iPhone).
But energy probably isn't the best measure to use anyway; you can deliver as much energy hitting it with a pillow as tapping it with a hammer, but you wouldn't expect a tuning fork to ring as loud. Peak acceleration might be better, but that still relies on good data from the accelerometer.
Could you use the microphone? Try recording what it hears when you tap it against you knee, and look for features that aren't present in ordinary sound, like, I don't know, big low-frequency amplitude, wide spectrum, maybe even a characteristic resonance of the case. It may still respond a little bit to a loud noise in the environment, but then that's quite realistic.