The service manual says you should measure the bore I believe 30mm down from the top edge where the head bolts on.
I just used a dial caliper from the top and from the bottom of the bore, I got the results I needed.
Write down that measurement.
You need a service manual to find out the max service limit for your year bore size. If it is not at the max service limit, and the bore is not all beat up, scratched and Nikasil flaking, then just hone it or scotchbrite it lightly, and be done with it.
Measure your piston, grab it from the top directly across the center with a dial caliper. Look for the largest number you can achieve with the calipers.
Write down that measurement.
Measure in many different places around the piston. Again, look for the service limits, and....then take the measurement of the piston and subtract that number from the masurement of the bore.
You need around .004-.005" difference, the piston smaller than the bore. Anything greater (example: .007") and the piston will slap in the bore.
I used a new Pro-X brand piston and rings that was .001" oversize in my 22 year-old KX500 bore. Worked great, I ended up with .005" piston to bore clearance. The Pro-X piston from Dennis Kirk was like $100.00
One of the most important things to do is to de-gunk your KIPS valves with oven cleaner before you start prying on them to get them out, clean the bores that they seat in, clean the valves, reset the valve timing per the manual.
Look for cylinder cracks in a bright light.
New gasket kit, etc.
If you need to re-plate your cylinder, send your new piston to the shop with the cylinder, they will mate them together for you perfectly.