OK, I got your problem:
Runout concentricity to cylinder bore realy is not critical, but removing a slight amount of metal to get the fit to the cooling jacket just right is important.
Here is what I would do:
Fit the mandrel in the 4-jaw.
Make strips of newspaper-paper, about 1/2" wide, and paste these to the madrel with a bit of grease. This paper is 0.002" thick, and should do well to get the right friction fit between mandrel and cylinder.
When satisfied, tap the cylinder on all the way and adjust the runout with the 4-jaw. If you want to be very precise, also check runout on the mounting flange to be sure the cylinder bore is wobble-free. I do however not think that is critical, because the bore should be perpendicular to that mounting face if your cylinder is OK to start with. Whichever way you fit that cooling jacket will not change a thing to bore-flange alignment.
On each check station, also check lengthwise integrity (straightness), so you will have no wobble. Tap- and adjust the mandrel in the jaws until you are satisfied with straightness and runout of the cylinder. When done, you should be within 0.002 T.I.R on all possible sections.
I did a similar thing in a 3-jaw. It took me quite a while. A 4-jaw is much easier to adjust.

The cooling jacket need not be a press fit. A smooth tight slide fit will do (thump pressure fit). The cylinder in operation heats up and expands right onto the cooling surface, as is the case in our glow engines.