This paper examines the ability of the field line interhemispheric plasma (FLIP) physical ionospheric model to reproduce the O+, NO+, O2+, and N2+ ion densities, and nitric oxide density in the ionosphere and thermosphere over Australia in September 1974. The study includes ionospheric electron density data from Australian ionosonde stations as well as ion and neutral density composition data from elliptical orbits of the Atmosphere Explorer-C (AE-C) satellite. The mass spectrometer and incoherent scatter (MSIS) neutral atmosphere model accurately reproduces the O and N2 densities during quiet periods in September 1974, and this enables the FLIP model to also accurately reproduce the measured ion and NO densities as well as ion and electron temperatures during quiet periods. However, the MSIS model produces poor results during the disturbed period of 15 and 16 September because it underestimates the increase in neutral temperature by several hundred degrees and the depletion of the O column density by a factor of 2. When the measured neutral densities are used in the FLIP model instead of MSIS densities, there is fair agreement between the measured and modeled O+, O2+, and NO+ densities above 200 km on 15 September, but the FLIP model overestimates the O2+ density below 200 km. The FLIP model is also in fair agreement with the NmF2 from the ionosonde and reproduces the measured O+ density on 16 September but severely overestimates the satellite measured O2+ and NO+ densities at all altitudes. As found in previous studies, the FLIP model was able to accurately reproduce a positive ionospheric storm that occurred during this period. An important result to emerge from this study is the observation that even during these severely disturbed periods the altitude distributions of the measured O and N2 densities can be reasonably well represented by hydrostatic equilibrium profiles. This suggests that the basic philosophy of the MSIS model remains intact and that it should be possible to improve the MSIS model storm behavior just by improving the specification of the neutral boundary densities and the exospheric temperature. The assumption of hydrostatic equilibrium also simplifies the task of deducing neutral composition from remote sensing.