How's the runout on the other end? If I recall correctly, these cylinder castings are symmetrical, and so can be swapped end for end. I would align the best end of the cylinder on the frame and cap the most off center end on the dead end. You may also have enough room to go to a slightly bigger piston and cylinder bore, to bring it back to concentric alignment.
Four jaws are wonderful tools, but can easily get you in trouble. I usually try to just spot face first to provide a check for centering, and do a small bore through to check co-axial alignment, before approaching final dimensions.
Hindsight is wonderful, isn't it ...... but yes I do believe this sort of thing has been done before, a time or three!