Neutron stimulated emission computed tomography (NSECT) is being developed as an experimental technique for diagnosis of element related disorders in humans. Preliminary experiments have demonstrated strong potential for clinical diagnosis of liver iron overload in patients. The technique's sensitivity to high concentrations of iron combined with its non-invasive tomographic acquisition ability gives it a unique advantage over other imaging methods. This work explores a tomographic clinical application of NSECT for diagnosis of liver iron overload and optimizes the acquisition system to maximize accuracy and minimize patient dose. Monte-Carlo simulations of the NSECT system have been developed in GEANT4 and used to determine quantification accuracy, detection sensitivity and patient dose for several different scanning and acquisition geometries in NSECT. The research performed in this work demonstrates that NSECT has strong potential for iron overload diagnosis in patients and provides a validated simulation tool which can be used to guide the development of future clinical NSECT systems.