has a rocker/valve tapping sound but as you said, sort of indiscriminate 'central' location. you can use a stethoscope (or a dowel to the ear) and you'll hear it midway down the cylinder.
the cyl was relatively ok. what I did was, i figured the original one was just an outlier, so i ordered a spare, and sent the other one back as defective. takegawa said it was not for our model.. which is bullshit, because they said it was for the Japanese only model CT125. the cyls are the same across all of them, all the way back to the 1st gen groms. 22 and later groms/monekeys I 'think' are different though. I know they are the same before 22, because prior to this i had a high compression 125 piston/cyl on it that was leftover from my '14 grom. (still have that setup saved, and the stock unmolested trail cyl/piston and a blown up takegawa 143 cyl/piston on hand)
However, webike agreed with me and refunded the 1st one saying it was indeed defective. . when the second one went i just gave up and ordered a yuminashi cyl/piston, haven't had an issue since. as in, a few thousand miles. never tried to get a refund ont he second setup. as a sidenote, i changed nothing else between the 3 cyl sets in regards to tuning or intake exhaust at the time. the one thing i changed was the cyl/piston which proved my point to me.
I don't feel as you did anything wrong, at all. But i'd almost bet your piston skirt collapsed a bit and that's what you are hearing. i guess you could always go with a different piston and get your cyl honed to work with it.