This research proposes a novel standalone multi-stage photovoltaic (PV) architecture for efficient and reliable water pumping in agriculture. Traditional pumping methods often suffer from high fuel costs, grid dependency, and environmental concerns. To overcome these, the proposed system integrates a switched-LC-based high-gain (SLHG) converter, a Li-ion battery for energy storage, a 3-phase 2-level voltage source inverter (VSI), a brushless direct current (BLDC) motor, and a centrifugal pump. The SLHG converter, achieving a voltage gain of approximately 3 at a low duty cycle of 0.3, enables the use of low-voltage PV sources while ensuring maximum power point extraction via a modified adaptable step-size incremental conductance (MASS-INC) MPPT method, which achieves an efficiency of up to 89.84% with a fast tracking time as low as 0.034 s. A Li-ion battery, managed by a bidirectional DC-DC converter, provides an energy buffer for uninterrupted operation during periods of low/zero solar irradiation. This study employs 120° trapezoidal electronic commutation control, where the stator windings are energized in a six-step sequence determined by Hall sensor feedback analyzed through Boolean logic. The proposed configuration is modeled in MATLAB/Simulink platform, and its performance is validated under steady-state and dynamic solar insolation conditions.