I also have a Koda 16 and had the same issue with toppings burning while the bottom wasn't cooked enough. This is what I do now to get around this problem.
1) Preheat the oven on the lowest temperature setting for 30 minutes.
2) Assemble the uncooked pizza, ready to deploy in the oven.
3) Take the uncooked pizza to the oven, turn the oven OFF, and deploy the pizza about in the middle.
4) Once the bottom sets up (maybe a minute or so), rotate the pizza on the stone keeping it in the back left corner where the burners are located. Rotate about 1/3 every 15 to 30 seconds to keep the bake even. Check the bottom for good color (eventually).
5) Move the pizza to the center of the stone, turn the oven ON at the lowest setting.
6) Turn the pizza every 15 seconds or so until the top looks done.
7) Take out the pizza and put it on a wire rack to cool for 3 or 4 minutes.
8) Move pizza to a cutting board, slice, paint the edges with garlic oil, sprinkle with oregano.
This flame off / flame on technique was a game changer in my pizza making quest. Good luck!