Your pictures make that pizza look mighty tasty.
Is that pizza made with the same recipe you used before? Did the texture come out okay this time?
Here are few things to consider, just looking at the recipe for the dough and your comments about cooking it:
1. 55% hydration is pretty high for Chicago thin/cracker-type crust, which is what V and N's pizza more closely resembles. I would definitely consider scaling this back to no more than 48%.
2. I have never used milk in my dough recipes, but I know Vito and Nick's does use it. I don't know if that has anything to do with the results you are getting or not. Baker's Dry Milk might be another way to go (which I have used and had good results).
3. You said you heat the stone at 550 degrees F in your oven on the bottom rack for 1 hour, then put the pizza on it and cook at 450 degrees F for 10-12 minutes, turning it 180 degrees about half-way through. Just from this procedure alone, here are some suggestions which you may want to try 1 at a time:
a. don't turn the oven down to 450 degrees, keep it at 550
b. don't turn the pizza half-way through - keep the oven closed and the heat in for at least 10 minutes
c. consider a different rack. Oddly enough, the rack that works best in my oven is the top rack. I guess it's that "heat rises" thing.
d. consider par-baking the crust for 4-5 minutes before adding the sauce and other toppings
Looking forward to hearing and seeing more of your experiments.