We develop a model for small scale structure in the midlatitude sub-auroral polarization stream (SAPS)-driven density trough ionosphere during a magnetic storm. We include the effects of ring current precipitation, parallel currents, rapid subauroral ion drifts, storm-induced neutral winds, ion temperature and density gradients. We find that ionospheric density, electric field, ion and electron temperature irregularities can be driven in the stormtime SAPS-driven density trough (1) wall region from the ion temperature gradient convective instability, which is driven by density and ion temperature gradients, in concert with the gradient-drift instability and (2) central region from an ion frictional heating instability which is driven by strong ion convection.