A combustion system includes a distal flame holder, a pilot fuel distributor, a main fuel distributor, an oxidant source, an array of sensors, and a controller. The oxidant source outputs an oxidant. The pilot fuel distributor supports a pilot flame configured to preheat the distal flame holder by outputting a pilot fuel at least when the combustion system is in a preheating state. The main fuel source outputs a main fuel in the standard operating state. The distal flame holder is configured to support a combustion reaction of the main fuel and the oxidant in the standard operating state. The sensors are configured to sense parameters of the pilot flame and the distal flame holder and to output sensor signals to the controller. The controller executes software instructions that include adjusting the flow of the main fuel, the pilot fuel, and the oxidant responsive to the sensor signals.