Spatial aperture coding is a technique used to improve throughput without sacrificing resolution both in optical spectroscopy and sector mass spectrometry (MS). Previous work demonstrated that aperture coding combined with a position-sensitive array detector in a miniature cycloidal mass spectrometer was successful in providing high-throughput, high-resolution measurements. However, due to poor alignment and field nonuniformities, reconstruction artifacts were present. Recently, significant progress was made in eliminating most of the reconstruction artifacts with improved field uniformity and alignment. However, artifacts as large as 1/3 of the main peak were still observed at low mass (<17 u). Such artifacts will reduce accuracy in identification and quantification of analytes, reducing the impact of the throughput advantage gained by using a coded aperture. The artifacts were hypothesized to be a result of a mass dependent in curvature of ions in the ion source. Ions with higher mass (m/z > 17 u) and a larger curvature did not pass through all slits in the coded aperture. Therefore, when reconstructing with a system response derived from the aperture image from a higher mass m/z = 32 u ion, reconstruction artifacts appeared for m/z < 17 u. In this work, two methods were implemented to significantly reduce the presence of artifacts in reconstructed data. First, we modified the reconstruction algorithm to incorporate a mass-dependent system response function across the mass range (10-110 u). This method reduced the size of the artifacts by 82%. Second, to validate the hypothesis that the mass-dependent system response function was a result of differences in curvature of ions in the ion source, we modified the design of the ion source by shifting the coded aperture slits relative to the center of the ionization volume. This method resulted in ions of all masses passing through all slits in the coded aperture, a constant system response function across the entire mass range. Artifacts were reduced by 94%.