I think the precise pulse energy is not important here. The value of A0 will be dependent on the measuring instrument (alignment, focus). The value should be guessed from the raw data. The important parameter here is FWHM which is independent of A0.
You can find some help on the Fourier transformation here
I am not sure what is your ultimate goal it but measuring the spectrum is more straight forward than the mathematics. Also for an transform limited pulse (Gaussian) the spectral width and temporal width is equal to 0.44.