put the 2 cylinders together headgasket-headgasket surfaces touching
clamp them so they are 1 long cylinder and the 2 bores are perfectly aligned. (this is where using a piston to align it comes in handy) don't worry about the rest of the cylinder. JUST ALIGN THE BORE.
hone away. slow speed, plenty of fuel on them
if you hone in an individual cylinder, the hone balls will scar the head gasket surface and will most likely cause a gasket leak.
John