THOR is the first open-source general circulation model (GCM) developed from scratch to study the atmospheres and climates of exoplanets, free from Earth- or Solar System-centric tunings. It solves the general non-hydrostatic Euler equations (instead of the primitive equations) on a sphere using the icosahedral grid. In the current study, we report major upgrades to THOR, building upon the work of Mendonça et al. (2016). First, while the Horizontally Explicit Vertically Implicit (HEVI) integration scheme is the same as that described in Mendonça et al. (2016), we provide a clearer description of the scheme and improved its implementation in the code. The differences in implementation between the hydrostatic shallow (HSS), quasi-hydrostatic deep (QHD) and non-hydrostatic deep (NHD) treatments are fully detailed. Second, standard physics modules are added: two-stream, double-gray radiative transfer and dry convective adjustment. Third, THOR is tested on additional benchmarks: tidally-locked Earth, deep hot Jupiter, acoustic wave, and gravity wave. Fourth, we report that differences between the hydrostatic and non-hydrostatic simulations are negligible in the Earth case, but pronounced in the hot Jupiter case. Finally, the effects of the so-called "sponge layer", a form of drag implemented in most GCMs to provide numerical stability, are examined. Overall, these upgrades have improved the flexibility, user-friendliness, and stability of THOR.