Absolutely blown away by how delicious this is!
Since I'm not a pepperoni fan, I subbed pepperoni for some bacon bits and used a small amount only for both stuffing and the topping. I also added sliced jalapenos (stuffing and topping) and sauteed baby bella mushrooms for the stuffing. For the cheese, instead of only mozzarella, I did half mozzarella and half cheddar.
On the top I put parmesan cheese last (shredded fresh Parm, not the powdery version) on top of the jalapenos, bacon bits, etc so that when it melts, it holds those ingredients together after baking.