Did you try bolting on the honing plate and measuring that way? If the bores are straight with the plate installed, then it suggests that the torque/honing plate does not adequately simulate the stresses of the actual heads. Also, did you try bolting on one head at a time and measuring the other side? Because most shops only have a single torque plate, they hone while that plate is on. Perhaps it would make a difference if both sides had torque plates installed simultaneously? Please post back if you try any of these things.
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