I realize the difference in these flours are going to require different formulas and mixing/kneading times to get the most out of each one. That would take an awful lot of trial and error experiments to complete, if in fact it ever could be complete with so many variables in play.
Steve, it can
get incredibly hairy when tweaking formulas for different flours. In commercial settings, it can take weeks to dial in a new, same protein content flour, and if they change to a different protein level, it can take months to obtain the desired results. In your particular instance, though, it need not be that complicated. This is, to an extent, what absorption values are for. While absorption values are rarely perfectly reliable, they're in a close enough ballpark to allow you better judge two flours of varying protein content side by side. Right now, when you compare occident (12.4% protein) and kyrol(14%) in the same formula, you're predominantly comparing a high relative hydration vs. a lower relative hydration and not really seeing the features of each flour side by side. I don't have the absorption values in front of me, and they might take some digging to find, but taking the difference between the two and subtracting the water from you current formula will go a very long way in leveling the playing field and allow you to get a much better idea of what each flour is capable of.
Even if you can't track down absorption values, just dropping the hydration by 3% for the lower protein flours will give you a far better flour vs flour viewpoint as opposed to a decreased/increased hydration perspective.
The 2 minute bake with malted, bromated (in 2 instances) flour definitely plays a role in texture. The puffier the crumb, the less propensity for toughness. Scott R talks about malted bromated flours bordering on being too puffy as you break the 2 minute barrier. If 2 minutes is where you want to be and you think malted and bromated is the direction you want to take, then perhaps the additional structure of the kyrol might be a benefit. Should you move up to 4, though, I believe that's where the lower protein flours generally tend to perform a bit better (in typical NY formulations).
One small thing to consider when working with malted flours in 2 minute-ish environments is that the sugar and intense heat will char the undercrust a bit faster than unmalted flour, and your window of being done/slightly charred and not incinerated will be smaller. It looks like, with your extensive oven tending experience, that you're pulling the pies at exactly the right time, but if you ever plan on hiring someone less experienced, malted flour at 2 minutes might be a problem.
Fat is key to a good cheese melt. Supermarket mozzarella will have less fat than food service (Grande/Grande clones) and supermarket part skim will have less fat than whole milk, Add in the drying/browning encouraging aspect of the anti-caking starch in pre-shredded cheese along with the intense heat of a WFO and you've got a recipe for disaster.
Foodservice mozz (from Norma or elsewhere) will make your life exponentially easier, but if you want to work with the supermarket stuff, as I said before, a drizzle of oil will be hugely helpful. When drizzling oil, you basically, on the plain pies, want to mirror the quantity of fat that's rendered from the pepperoni. Water can be helpful as well. Not only does water slow the cheese from browning, it helps the cheese to bubble. Water isn't as effective as oil, though, and you have to be careful not to use too much or you'll jeopardize the stability of the cheese. 2 or 3 mists from a $1 sprayer over the cheese area should do the trick.