When I made all of the PJ clone pizzas, I tried to replicate as closely as possible the baking method used by PJs, which entails using a pizza screen and an oven temperature of around 475-500 degrees F. I used only a pizza screen, not a combination of pizza screen and pizza stone as you did. I have found that in my basic builder's grade electric oven I do not get particularly good results using a pizza screen directly on a preheated pizza stone. The oven spring is not as good as when I use the pizza screen by itself and it can take quite a bit longer than normal for the pizza to bake to its final desired condition. This is with a pizza stone that has been preheated on the lowest oven rack position for about an hour at about 500-525 degrees F.
I believe that in your case, with only a 35 minute preheat of your pizza stone, that slowed down the bake even more and was perhaps largely responsible for the results you achieved. If I were to use a combination of a pizza screen and a pizza stone to make a PJ clone pizza, I would place the pizza stone on the lowest oven rack position and preheat it for about an hour at about 500 degrees F. I would then place the unbaked pizza on the pizza screen and bake it at a higher oven rack position until the rim forms and starts to turn a light brown (the cheeses will also usually be bubbling and maybe even turning a light brown depending on the particular cheeses used). I would then move the partially baked pizza off of the screen and onto the pizza stone to finish baking and to develop better bottom crust browning. If, after the bottom crust is nicely browned but the toppings are not yet fully baked, I would move the pizza back to a higher oven rack position to get additional top heat to finish baking the pizza.
In your case, I don't think it was the toppings or cheeses that were responsible for the partially unbaked crust even though, at about 10 ounces of cheese, that would be a few ounces greater than what I believe PJ uses for a 14" pizza (I estimate around 7.5-8 ounces for a basic pizza). I believe your problem was related to the oven thermodynamics.
There are some members who have made the PJ clone pizzas using only a pizza stone. I did not try this method myself, as I noted earlier, but such members apparently got good results. However, in using the pizza stone, care should be taken to be sure that the bottom of the crust does not brown too quickly or excessively before the rest of the pizza is finished baking. This may mean having to move the pizza higher in the oven to get the pizza a safe distance from the bottom coil.
Your alteration of the recommended fermentation of the PJ clone dough should not have made a huge difference that I can see. However, those changes, coupled with the specific bake protocol you used, might have produced a finished product that less resembled an authentic PJ pizza. Just changing the bake method can do that.
Should you adopt any of the above recommendations, please keep us informed of your progress or any other problems that might develop.