The reason I asked you where you are located is that flours used outside of the U.S. are often weaker than U.S. flours and don't perform in the same fashion, and often with the same degree of success, as U.S. flours . High-gluten flours, which is the type of flour called for by Canadave's recipe, are often unavailable in many countries outside of the U.S. Substituting bread flour will often work, but substituting all-purpose flour, even if supplemented with vital wheat gluten (VWG), doesn't produce equivalent results. Moreover, when using weaker flours, it is usually necessary to alter the hydration value of the recipe such that it approaches the rated absorption value of the particular flour used. In the U.S., for an all-purpose flour, that hydration value would be around 60%. That is what I mean by "hydration control".
In your case, you may want to lower the hydration value to around 60% and make whatever ancillary adjustments are necessary if you plan to supplement your flour with VWG and/or whole wheat flour. If you are using, or plan to use, only whole wheat flour, possibly supplemented with VWG, I can't tell you how well Canadave's recipe will work with that flour blend.
If you use bowls instead of freezer bags, you should avoid the need to re-ball, re-shape or re-knead the dough balls. Under normal conditions, you never want to do this sort of thing. It sounds like you are trying to make four 12" pizzas rather than two 16" pizzas. If such is the case, you shouldn't have any problems making four 12" pizza.
By bake protocol, I meant how you baked your pizzas, that is, using a pizza stone or tiles or screen, the type of oven, the rack positioning, oven temperature and bake time.