The NY style dough recipe you posted comes from here: http://www.recipepizza.com/doughs/ny_style.htm
I was neither impressed with the write-up or the dough recipe itself, which I deem to be flawed or problematic in several respects, to wit:
1. Adding the yeast called for by the recipe, which I assume to be instant dry yeast (IDY), to the rest of the dough ingredients after they have been combined does not make a lot of sense. That method is often used to make bread doughs that are first subjected to an autolyse rest period. However, no such autolyse is called for in the recipe. Pizza operators who use IDY, whether for a NY style or any other style, add the IDY to the flour. If you used ADY as you indicated and added that to the dough as called for by the recipe, that is even more problematic. For best results, the ADY should be rehydrated in a portion of the formula water at about 105 degrees F for about 10 minutes. The rehydrated ADY can then be added to the rest of the formula water, which ideally should be on the cool side.
2. If one-half teaspoon IDY is used for 4 1/2 cups of all-purpose flour, there is no way that you will be able to use the dough in 1-2 hours. One-half teaspoon of IDY for 4 1/2 cups of all-purpose flour measured out the way you indicated comes to about 0.20%. Unless you use water at a temperature just short of being able to kill the yeast (about 143 degrees F), and/or your kitchen is around 110-120 degrees F (I am somewhat guessing on this), you won't get sufficient fermentation activity to use the dough within 1-2 hours. 0.20% IDY should work for cold fermentation purposes although it may be a bit on the low side based on the flour measurement method you used.
3. The recipe calls for using 18 ounces of dough for a 12" pizza and 25 ounces of dough for a 15" pizza. Those numbers translate to thickness factors of 0.1592057 and 0.141492, respectively. The thickness factor of a typical NY style pizza dough is between about 0.085-0.10. Your dough skin would be too thick by NY pizza style standards. That may also explain the long recommended bake time (20-25 minutes). It takes a long time to bake very thick crusts so it is no surprise that the cheeses would break down during the protracted bake time, especially with a 500 degrees F oven temperature. If you used several toppings and/or a lot of cheese, those steps would further aggravate matters. A typical NY style pizza baked in my home oven takes about 6-7 minutes on average.
It is possible to fix the recipe you used and the instructions for the recipe, but it is sometimes better to just find a good, proven NY style dough recipe to begin with. With respect to the whole wheat dough recipe, you might want to look at the whole-wheat dough recipes posted on the forum under the Specialty-Grain Pizzas board.