The standard cosmological and particle physics models (ACDM and the Standard Model) currently face insurmountable observational tensions, notably the Hubble constant discrepancy, the surface brightness anomalies of high-redshift galaxies detected by JWST, and the persistent g-2 anomaly. This comprehensive paper introduces the Primary Energy (PE) Theory, a unified phenomenological framework that models the physical vacuum as a material, viscous superfluid substrate. By abandoning the geometric abstraction of empty spacetime in favor of a hydrodynamic medium, we derive a set of macroscopic and microscopic viscosity parameters that naturally resolve these crises. We demonstrate that cosmological redshift is a cumulative dissipative effect in a wave-regime vacuum (eta_wave ~ 0.10), which precisely accounts for the Hubble tension. Cross-correlation analysis of raw LIGO data (GW150914) reveals a previously undetected frequency-dependent dispersion lag of ~21.2 ms, yielding a micro-viscosity coefficient (eta ~ 2.02 x 10^-9) that correlates fundamentally with quantum electrodynamic radiative corrections (alpha^4). Furthermore, we introduce a dynamic gravitational constant, G_eff, which mathematically eliminates metric singularities in black holes. Finally, we propose two falsifiable experimental protocols to test the local saturation limit of vacuum viscosity (eta_max ~ 0.14) at a critical magnetic field threshold of 17.5 T: the static muon decay test and a noise-resistant nuclear metrology protocol utilizing the Thorium-229 isomer.