Abstract: Outward transport of cold iogenic plasma in Jupiter’s inner magnetosphere is governed by the interchange instability, which is highly sensitive to the spatial structure of the Io plasma torus. Using the Rice Convection Model–Jupiter, we investigate how phase shifts in density perturbations, whether imposed initially or induced by background velocity shear, affect interchange convection. A series of runs explores the respective effects of imposed phase shifts and background velocity shear on both a prescribed Io torus and an active Io source. We find that while these factors do not alter the overall evolution of convection, they strongly modulate its morphology and dynamics. Phase shifts suppress the interchange instability early on, regulating plasma flow and triggering a structural bifurcation: small phase offsets yield single interchange fingers, whereas larger offsets produce double-finger structures. This influence markedly diminishes by the quasi-steady stage. Background velocity shear suppresses instability via two intertwined mechanisms, inducing phase shifts (dominant early) and reducing local angular velocity (more prominent later), which are often difficult to separate.