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The SISSI/SGCI framework (Spectral Information Similarity System Interface / Spectral Generalized Coherence Index) provides a unified harmonic–geometric model for quantifying vibrational information flow across molecular systems. While Version 1 introduced the mathematical formulation of the harmonic operator and its coherence functional, this Version 2 presents the first real-world experimental validation using isotopic vibrational spectra. Benzene vs. benzene-d6 and water H2O vs. heavy water (D2O) serve as benchmark systems to test sensitivity, robustness, and harmonic alignment performance. We introduce a fully reproducible end-to-end pipeline including JCAMP-DX parsing, baseline correction, normalization, uniform resampling, local harmonic curvature mapping, sliding-window coherence tracking, zero-matching distance (ZMD), and Monte Carlo null-model comparison. Results show that SISSI/SGCI identifies isotopic vibrational shifts with significantly higher precision than classical spectral similarity measures (correlation, cosine similarity, RMS error), and remains stable under synthetic noise conditions. This experimental validation demonstrates that SISSI/SGCI is not only a mathematically rigorous formalism but also a practical high-resolution tool for analyzing vibrational information, with potential applications in spectroscopy, materials science, computational chemistry, and information-theoretic descriptions of molecular dynamics. All datasets, figures, and the complete reproducible demonstration package are openly released.