Yes, it is most likely the culprit. I had that motor apart twice now, and I've done enough fours that I know I did my part correctly. That's where I made the mistake. The machinist I used was the only guy local who had a boring machine small enough, and he can highly recommended. He was very familiar with these motors (or so I thought), and I never measured the clearance afterward, that is my fault. Mark thinks he likely went to something like .0020 rather than the .0008 it should be. The pistons are the cruzin image ones. There is a silver lining, I am going to source a new set of barrels, and I have a 3mm overbore kit sitting on a shelf. Since Mark's machinist seems to be "the guy" to get it right, I will send it to him.
There is nothing I hate more than doing something twice, especially when it's because of someone else's work. I will never assume again though, that's for sure.