In general, I have not had any problems in getting smooth and cohesive PJ clone dough balls. The particular PJ clone recipe you used, which is set forth at Reply 2 at http://www.pizzamaking.com/forum/index.php/topic,6758.msg58197.html#msg58197,
produces a dough with an "effective" hydration of 63.8%, which I calculated by adding the formula hydration (56.5%) and the formula oil (7.3%) together. That value is close to the rated absorption value of a high-protein flour. As a result, using a basic KitchenAid stand mixer or using hand kneading produces a somewhat underkneaded dough that is easy to form and shape into nice, round cohesive balls. I, too, have a Zojirushi bread maker but have not used it to make a PJ clone dough. However, I know from having used that machine to make other types of doughs that it is important not to overknead the doughs. That can result in drier doughs that are somewhat harder to form into nice tight balls without knots and other irregularities. I have also learned from working with different types of doughs that the doughs with the highest hydration values tend to be the easiest to shape and form into tight, smooth dough balls.
There are many videos and articles on how to shape and form dough balls. A couple you might want to look at are the Bruno's video at
and the Lehmann/Zeak video at
I calculate that the "effective" hydration of the Bruno's dough, which is said to be a NY style dough, is around 54.2%. That is on the low side, and if you look at the dough ball shaping steps starting at around 5:45, you will see how it is a challenge to form the dough balls so that they are tight without seams, knots and the like. By contrast, if you look at the comparable steps in the Lehmann/Zeak video, starting at around 3:02, you will see that the dough balls are formed more easily. I suspect the reason is that the Lehmann/Zeak dough balls have a higher effective hydration. Another video, by Tony Gemignani, that shows similar dough forming methods, can be seen at
You can also see one method of how Neapolitan-style dough balls can be formed at http://www.woodstone-corp.com/cooking_naples_style_dough.htm.
If you click on the photos, you can see them in enlarged form. The dough balls shown in the article have a hydration of 55.6%. That is fairly close to the rated absorption value of 00 flour and should allow one to make good, tight dough balls.
Ultimately, it is likely to be practice that allows you to make nice, cohesive, tight dough balls. In your case, with your Zo machine, you might want to keep the kneading down to a minimum (you want the dough to be slightly underkneaded) so that you don't overly develop the gluten and end up with a dough that is dry and harder to form into dough balls.
EDIT (6/14/16): For a Wayback Machine version of the above inoperative Woodstone link, see http://web.archive.org/web/20090215125027/http://www.woodstone-corp.com/cooking_naples_style_dough.htm