Can't you just bore some jaws with a step to locate the end of the part? The face of the step would be Z0. Program the first side by adding a stock value to all your Z coordinates, so the finished front face of the first side would have a program Z value of the overall length of the part plus something to leave for cleaning up the second side. The front face of the second side would have a program Z value equal to the finished overall length of your part.
Added bonus - the step will prevent the part from pushing back in the jaws when you're taking a roughing cut.
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