A recently developed magnetic molecular interferometry technique allows the experimental determination of how the amplitudes and phases of the molecular wave-function change during the collision of a gas phase molecule with a surface. This information, quantified by a scattering-matrix, provides a very stringent benchmark for developing accurate theoretical models as they can also be determined from scattering calculations and are particularly sensitive to the underlying interaction potential. However, the value of this comparison is necessarily limited by the accuracy with which an empirical scattering-matrix can be extracted from the experimental data. This paper presents the methods used to analyse the measurements and uses simulations to determine how various uncertainties in modelling the different magnetic elements which make up the beamline of the apparatus affect the accuracy with which the scattering-matrix can be extracted. It is shown that when signals have a noise level which corresponds to on the order of 1% of the oscillation amplitude, the uncertainties in the modelling do not significantly affect the ability to extract the scattering-matrix elements, with the error in the extracted values increasing to a few percent as the noise in the signals is increased to 10% of the oscillation amplitude. This therefore gives an estimate of the accuracy of the parameters that can be obtained from future measurements.