A method of operating a gas discharge excimer laser having a master oscillator portion, producing narrow band seed laser light output pulses and a power amplifier portion, receiving and amplifying the narrow band seed laser light output pulses into power amplifier laser light output pulses, operating at power amplifier laser light output pulse repetition rates greater than or equal to 4000 per second, in a burst of pulses during an on period, followed by an off period, and having an electrical discharge pulse power system converting energy stored on respective master oscillator and power amplifier charging capacitors into electrical discharge pulses across gas discharge electrodes in each of the master oscillator and power amplifier, through a respective master oscillator and power amplifier multi-stage electrical discharge magnetic pulse compression circuitry and electrical discharge pulse fractional turn voltage step-up transformer, comprising: in a primary layer of control adjusting at least one of: an amount of energy stored on the respective one of the master oscillator charging capacitor and the power amplifier charging capacitor by selecting a respective charging voltage for the master oscillator charging capacitor and for the power amplifier charging capacitor by scaling the target energy by dV/dE to get the respective charging voltage; or a timing of the electrical discharge pulses in each of the master oscillator and the power amplifier based upon a respective commanded charging capacitor voltage determined for an upcoming electrical discharge pulse in each of the master oscillator and the power amplifier, wherein a timing correction for each of the master oscillator and the power amplifier is calculated by passing said commanded charging capacitor voltage through a delay estimation formula. in a primary layer of control adjusting at least one of: an amount of energy stored on the respective one of the master oscillator charging capacitor and the power amplifier charging capacitor by selecting a respective charging voltage for the master oscillator charging capacitor and for the power amplifier charging capacitor by scaling the target energy by dV/dE to get the respective charging voltage; or a timing of the electrical discharge pulses in each of the master oscillator and the power amplifier based upon a respective commanded charging capacitor voltage determined for an upcoming electrical discharge pulse in each of the master oscillator and the power amplifier, wherein a timing correction for each of the master oscillator and the power amplifier is calculated by passing said commanded charging capacitor voltage through a delay estimation formula. an amount of energy stored on the respective one of the master oscillator charging capacitor and the power amplifier charging capacitor by selecting a respective charging voltage for the master oscillator charging capacitor and for the power amplifier charging capacitor by scaling the target energy by dV/dE to get the respective charging voltage; or a timing of the electrical discharge pulses in each of the master oscillator and the power amplifier based upon a respective commanded charging capacitor voltage determined for an upcoming electrical discharge pulse in each of the master oscillator and the power amplifier, wherein a timing correction for each of the master oscillator and the power amplifier is calculated by passing said commanded charging capacitor voltage through a delay estimation formula.