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The low-pass characteristics of front-end elements including light-emitting diodes (LEDs) and photodiodes (PDs) limit the transmission data rate of visible light communication (VLC) and Light Fidelity (LiFi) systems. Using multiplexing transmission techniques, such as spatial multiplexing (SMX) and wavelength division multiplexing (WDM), is a solution to overcome bandwidth limitation. However, spatial correlation in optical wireless channels and optical filter bandpass shifts typically limit the achievable multiplexing gain in SMX and WDM systems, respectively. In this paper, we consider a multiple-input multiple output (MIMO) joint multiplexing VLC system that exploits available degrees-offreedom (DoFs) across space, wavelength and frequency dimensions simultaneously. Instead of providing a new precoder/post-detector design, we investigate the considered joint multiplexing system from a system configuration perspective by tuning system parameters in both spatial and wavelength domains, such as LED positions and optical filter passband. We propose a novel spatial clustering with wavelength division (SCWD) strategy which enhances the MIMO channel condition. We propose to use a state-of-the-art black-box optimization tool: Bayesian adaptive direct search (BADS) to determine the desired system parameters, which can significantly improve the achievable rate. The extensive numerical results demonstrate the superiority of the proposed method over conventional SMX and WDM VLC systems.