OK you have slightly different advice on bottom end... what to do with all this info is up to you
Let's talk top end. I’ll start it off
If the engine is running now how quiet

is the top end while running idling at 1500 -2000 rpm?
Is it noisy, rattling, scuffing or slapping? If
not your top end may be fine. It gets no better than a quite smooth running top end.
Check compression. See how well balanced the two side are. Once you take the top end off keep everything together. Check the cylinder liner top for a ridge. This is where the top rings stops at its highest point. You may have some carbon and rust above that point so you need to clean up to see if a true ridge. When I say ridge I mean wear in the actual metal of the liner. If there is distinct ridge you can see of feel , cylinder is worn. Check around ports at middle area look for wotn concave areas or lips. Hold to sun light and these areas will reflect light differently.
Your cylinder will always have some wear versus new but if little I let it go especially if it is running smooth, quiet and even compression as explained.
There are tools do this per the book (measure wear like a pro or pros) but your eye can tell you a lot. If the cylinders and piston don’t have significant signs of scuffing you may be able to reuse. And, it's already fitted in well. Not often do I find them like this but I do and enjoy.
Check the rings for gap too large cylinder worn and/or rings warn. It can be just rings more so than lines but if you change just rings (very common low buck method)) you will have to deglaze liner (skip down to that below)
A little fine scratches about the ports, I would not worry. A top end is an easy job to do later. In this rare but plausible case liner OK I just clean up carbon and put back together as it was. I don’t not touch cylinders and leave them as is with their wonderful slipper oil glazed liners.
I will alway renew wrist pin, wrist pin bearing and clip
Now the piston. If the tops looks like it is starting to decay/erode/ you have to replace. At this point I'll change rings too. If I feel the liners are in spec I'll go standard size. I use a cleanup brush or ball hone to deglaze the nice oil film off liner just so new rings will seat, that's it. Go no deeper. Don't try to remove all the scratched for all you have done is make is a larger clearance and that results in the quiet top end being noisy due to added piston slap top end noise. On air cooled engine it is sensitive and you will learn to dislike that sound amplified by the cooling fines and vibrations in you body as you ride. Going standard size new piston you are not trying to make cylinders like new. That’s next
If there is too much wear ,over sizing the bore to match a new piston set is advised. My most common choice, but it is not without risk (analogous to a surgeon performing an operation). Talk to your machinist of choice and discuss what he/she uses for equipment and how they do the process in steps. Tell them it is important to you that it fits per spec. Anyone with proper tools can do a good job. It is just not automatic (some new hone machine are more so today, but who has?) and requires the operator to take their time and measure a few times as they get near then end.
Next is carburetor!