Axisymmetric magnetic equilibrium reconstruction is insufficient for describing several effects in the Madison Symmetric Torus (MST). Inclusion of the field error produced by port holes in the close-fitting conducting vacuum chamber enables accurate interpretation of data from several subsystems, in particular, ion trajectories of a heavy ion beam probe and radial displacement and distortion of power deposition from RF antenna heating. In this work, an analytic solution for the magnetic field error produced by a port hole is added to the equilibrium. Without inclusion, the beam trajectory can deviate by over a centimeter (on the order of the detector width) at the analyzer apertures. In addition, the deposition layer for an electron Bernstein wave is strongly altered up to one port diameter away from the port hole.