If the end face was machined at the same setting as the bore which the OP suggests it was then I would not want to be using that to reset the work, the bore looks to run at an angle to the port face of the casting so that face will also be at an angle..
I would get the port face machined first and use that as the ref face. This can easily be done in the 4-jaw as two opposite jaw slots act like a Vee block for the flanges to sit in and a rule can be placed across the port face to get it at right angles to the lathes axis in the other direction. Now face the surface flat.
Ideally this flat face can then be held against an angle plate fixed to the faceplate to set the part square in one axis and a square used against the two flanges to set it true in the other axis before it is clamped tightly to the angle plate. You can now tap the lightly bolted angle plate about until the outside of the flange runs concentric and when it does tighten the angle plate to the faceplate and you are ready to bore and face. If you don't have an angle plate then the 4-jaw can be used with a square to ensure the port face is at right angles to the chuck face and also against the two flanges to make sure it is not twisted.
Plugging or clocking the flange is OK but you can't clock the other end true so end up with exactly what the OP has – hole central to one flange and well off by the time it exits the other end.
J
PS this also happens to be the way all the Stuart booklets tell you how to machine a cylinder casting.
Edited By JasonB on 23/03/2018 12:28:26