The piston on my CT2 has #965 on the top. I understand that #96 is standard. Can someone clear up the extra digit on mine? I assume 

it's oversize but first, second?  Thanks for any help.

Without pictures and precise measurements, I can't be 100% certain, with that in mind... 

"965" generally would mean the piston was 65.965mm when new....  or "standard size". 

Outside of cylinder skirt that drops into case might have something like "003" printed on it in ink which means original bore was 66.003mm 

The difference between the two was the original piston to bore clearance. 

A good machinist really should measure the bore for wear, out of round, and taper per the the manual.  Then a determination on what oversize it needs to be bored to, if any, can be made. 

I'll guess that the 5 is halfway between 96 & 97 clearance. Nothing to worry about.
It's still standard if i confused the issue.

Thanks for the help. I may pull the barrel and do a measurement.

Mark and RT325 touched on this, but genuine Yamaha oversize pistons will have the oversize stamped on the top - eg .25, .5 etc. Also, genuine oversize rings will have the same markings on them.