The EOM was tuned to have maximum input transmission. Now the output/input power is 1.846  mW / 1.866mW = 98.91 %.

The EOM was placed in cross polarizer configuration to be characterized.The setup is shown in Fig 1.

After this the resonant circuit was used to provide voltage to EOM from 10Vp-p to 0 at 335kHz.

The response of the laser incident on the photodiode after interaction with the EOM was recorded.

The plot is shown in Fig 2.

The specs during saving the peak value at resonant frequency.

151 mHz minimumum for hamming window. Number of frame averages = 10. See Fig 3 for any redundant details.

The conversion from PD voltage to power is done using

Voltage/Responsivity/TransimpedanceGain = Input Power

I am confused, as to how the transmission is 98.9% but in cross polarizer configuration is way less. Although, the circuit provides more than half wave voltage, even after considering losses.