This paper introduces a high-dimensional, measurement-device-independent quantum key distribution (MDI-QKD) protocol designed to overcome the limitations of "photonic flightiness" in long-distance fiber networks. By utilizing biphoton qutrits, the system achieves a robust unconditional security threshold of 17.7%. The architecture features a Transduction Triad that integrates biophoton signaling, DNA fractal antennas for physical layer security, and itinerant Surface Acoustic Wave (SAW) phonons for long-lived quantum memory. To manage system drift over a 90 km transmission link, we employ a 6-degree-of-freedom (6D) diagnostic framework optimized by the LOTUS-QAOA scheduling algorithm, resulting in a 27.2% improvement in expectation values. The protocol is anchored at the Planck Scale, establishing Topological Silence Zones that protect molecular-level encoding from decoherence and external signal injection. Experimental validation is supported by 2026 blind-test protocols utilizing Superconducting Radio-Frequency (SRF) cavity infrastructure and GNT → WMN mapping for waveform stabilization.