I'm measuring an old XR200 piston with a Performance Tool digital caliper. $5.00 at a garage sale, and worth every penny.
The wrist pin is 14.97mm, so we're off to a good start. The measurement from the bottom of the skirt to the piston top depends on whether you include the pop-up; 49mm without the pop-up, 50.20 with.
Center of wrist pin to piston top: 25.45mm / 27.05mm (approximate)
Top of wrist pin to piston top: 18.20mm / 19.77mm (approximate)
It looks like a Honda piston would be considerably higher, so I sure wouldn't plane the cylinder. Wiseco pistons to match the XR200 are available in 65.5mm, 66mm, 66.5mm and 67mm. Do you plan to bore out the cylinder?
Do you have an OHC engine? If so, perhaps a Honda cylinder would fit, which would allow you to run a bigger bore without machining costs.