What's it like at 1/4, 1/2 and 3/4 of the way down the bore and the measurements 90* to what you are measuring?
Also, can you post the diameter of the piston?
If you put a torque plate on and try to straighten the bore I'd bet it will take .004-.006 to get it straight. That's a lot. That would put you .007-.008 over nominal.