OK, this is a lot to process, but one thing that really sticks out to me is 9% oil. That's a lot of oil, especially for something with 62% hydration. I've never had CPK (and I probably never will), so I don't know what their crust is like, but I really doubt that it has anywhere near that much oil. With that much oil, it looks like you're making something more akin to a deep dish kind of dough. But deep dish hydration levels tend to be in the 40s, so this looks like a nightmare dough to me already.
Also, that's a ton of sugar and a ton of salt. And considering how much salt there is, the salt probably keeps the small amount of yeast from doing its job.
Honestly, this formula does not make any sense to me. I wouldn't even think about trying it because I would expect pretty much the same results you've described here. If I was actually able to make a usable dough out of it, I'd expect it to end up eerily dark, due to the ridiculous amount of sugar. And considering the high percentages of sugar, salt, and oil, I wouldn't want to taste it.
1. I'm using Rex Royal flour. I'm guessing the high protein is the reason this recipe required so much more flour. How do I compensate for this, for example when a recipe calls for regular bread flour? Do I just lower the hydration level?
OK, unless I'm reading this wrong, the first part here is counterintuitive. High protein flour can hold more water than lower protein flour. Your last sentence makes sense, though, sorta. Since bakers' percents are based on flour weight, yes, you should decrease the hydration level. That is, if you're gonna keep the oil at 9%. (Don't change the flour quantity in relation to all the other ingredients because that changes everything.)
I still don't understand the benefits of a higher hydration level on a cooked pizza. Is it less dense? I did notice last pizza I made that was more hydrated then usual, the bottom of the pizza had the circle texture on it which I notice at some pizzerias.
2. I'm using a pizza stone. My oven only goes up to 450 which is problematic for the bottom of the pizza. I was thinking of using a pan, though I don't understand the benefit compared to a stone? It seems easier because you don't need a peel which causes a lot of problems for me.
Like I said, I've never eaten at CPK, but I'm 99% sure CPK bakes directly on stone. So if you bake on a pan, you're not gonna come close to replicating their pizza. The difference: When you peel dough onto a hot stone, the bottom of the dough immediately starts baking. Conversely, when you use a pan, the bottom of the dough does not start baking until the cold pan gets hot. And even then, it doesn't bake the same way it bakes when you peel it onto a hot stone. In a home oven, you're gonna have a much longer baking time when using a pan.
3. When using ADY and the recipe calls for IDY I have been halving the amount. Is this correct? Aside from not having to proof the yeast, what is the difference with IDY? What is the end result affect?
If you're using ADY instead of IDY, you want to use about twice as much, not half as much.
It looks like you've translated someone else's recipe or formula here. Is that true? This thing is a mess, dude.