If this was a 72cc motor, I'd say measure the bore first. But, the tiny bore size of the 49cc version of our fave engine has an advantage...the piston skirt, proportionally, is very long. For that reason, we see a lot of 39mm cylinders that are still within spec. You don't want to actually hone the cylinder, technically speaking that means taking it out precisely to a finished size. All you want to do is de-glaze it...give it a light cross-hatching, to seat the new rings. That's a very quick process, few seconds with a drill & dingleberry hone. As long as you see a uniform surface finish, top-to-bottom, you're good to go. OTOH, if you see score marks, the rings will never seal and it'd be time for an overbore. And, that's the most common reason for taking a z50 cylinder oversize...unlike the bigger (47mm & up) versions which are more likely to be worn beyond spec.