I am about done with the essential repairs to this bike and was looking in the cylinder with my bore scope.
I can see the arrow on the piston with just a small amount of carbon on portions of the piston dome.
I can also see cross hatching that looks fine and no scoring but I do see "marks" on both sides of the cylinder where the wrist pin is. 
The "marks" don't appear to be gouging or scoring but more like discoloring.
Is this the normal look I should expect?
If this was a 4 stroke I would be alarmed but I would not expect to see an issue on both sides, usually just one side if a wrist pin decided to migrate one direction.
FYI-I have fired up the bike 3 times since I've had it, using the black wire method to the Emgo coil, with a hanging fuel bottle with a 40:1 premix in it and it fired right up easily all three times and made that sound we love with no abnormal noises. Run time was maybe one minute each time.
Presently waiting on a H4 6v headlight bulb that is lost in USPS limbo to test the complete wiring/charging system and do an oiler output test.
 

If it were a diesel engine, I would be saying that the engine had slightly overheated at some point and started picking up around the pin bosses.  Or another less likely scenario in your case, someone had fitted thrust buttons to the pin instead of circlips and they were a little tight.  Pretty impossible to do in a ported two stroke.

Or a bent rod.... 

However it is not a diesel engine, so if it has good compression and no horrible noise, put your boroscope away on the shelf to gather dust and enjoy the ride.