The cylinder should also be honed before assembling it, but not with a fixed stone hone. You should use a "flex-stone" ("spring ball", "bottle brush") like the one pictured below and at this link:
Lube the hone with solvent, and turn it at about 500 rpm. To use it, insert it into the cylinder and as soon as you start the drill, begin running the hone up and down the bore so that one pass down the bore, up the bore, and back down again takes about 1 second. As you make the 4th pass back up the cylinder, pull the hone out of the bore before stopping the drill.
The cylinder will now have the glaze broken in a cross hatched pattern, and if the wear at the top is not significant, the shadows will be gone as well. This process removes virtually no material from the cylinder, but puts down a surface in which the rings will seat almost as soon as the engine starts.
Clean the cylinder thoroughly with solvent. Then follow up by wiping the bore with a clean, lint free cotton cloth and some ATF (auto trans fluid). You'll be surprised how much the ATF will lift out of what you though was a clean bore.
This is the best reference of a previous post that I can find....where is the link/procedure that is mentioned in another post, or will the above mentioned just about cover it???