Hi Ivan,
Can you describe a little more how the Raman scattering is not accurate? You want to isolate the generated Raman signal from the input signal or just view the total output signal?
The EDFA spectrum can change from a couple of factors. For example, inhomogeneous broadening (spectral hole burning) of the spectrum could reduce the gain at the peak (if a high power signal is present) and thus shift the apparent peak to a different frequency.
Regards