A growing multispectral database plus recent Galileo descent measurements are being used to construct a self-consistent picture of the Jupiter thermosphere/ionosphere system. The proper characterization of Jupiter's upper atmosphere, embedded ionosphere, and auroral features requires the examination of underlying processes, including the feedbacks of energetics, neutral-ion dynamics, composition, and magnetospheric coupling. A fully 3-D Jupiter Thermospheric General Circulation Model (JTGCM) has been developed and exercised to address global temperatures, three-component neutral winds, and neutral-ion species distributions. The domain of this JTGCM extends from 20-¿bar (capturing hydrocarbon cooling) to 1.0 ¿ 10-4 nbar (including auroral/Joule heating processes). The resulting JTGCM has been fully spun-up and integrated for ≥40 Jupiter rotations. Results from three JTGCM cases incorporating moderate auroral heating, ion drag, and moderate to strong Joule heating processes are presented. The neutral horizontal winds at ionospheric heights vary from 0.5 km/s to 1.2 km/s, atomic hydrogen is transported equatorward, and auroral exospheric temperatures range from ~1200--1300 K to above 3000 K, depending on the magnitude of Joule heating. The equatorial temperature profiles from the JTGCM are compared with the measured temperature structure from the Galileo ASI data set. The best fit to the Galileo data implies that the major energy source for maintaining the equatorial temperatures is due to dynamical heating induced by the low-latitude convergence of the high-latitude-driven thermospheric circulation. Overall, the Jupiter thermosphere/ionosphere system is highly variable and is shown to be strongly dependent on magnetospheric coupling which regulates Joule heating.