While 3$d$-containing materials display strong electron correlations, narrow band widths, and robust magnetism, 5$d$ systems are recognized for strong spin-orbit coupling, increased hybridization, and more diffuse orbitals. Combining these properties leads to novel behavior. Sr$_3$NiIrO$_6$, for example, displays complex magnetism and ultra-high coercive fields - up to an incredible 55~T. Here, we combine infrared and optical spectroscopies with high-field magnetization and first principles calculations to explore the fundamental excitations of the lattice and related coupling processes including spin-lattice and electron-phonon mechanisms. Magneto-infrared spectroscopy reveals spin-lattice coupling of three phonons that modulate the Ir environment to reduce the energy required to modify the spin arrangement. While these modes primarily affect exchange within the chains, analysis also uncovers important inter-chain motion. This provides a mechanism by which inter-chain interactions can occur in the developing model for ultra-high coercivity. At the same time, analysis of the on-site Ir$^{4+}$ excitations reveals vibronic coupling and extremely large crystal field parameters that lead to a t$_{2g}$-derived low-spin state for Ir. These findings highlight the spin-charge-lattice entanglement in Sr$_3$NiIrO$_6$ and suggest that similar interactions may take place in other 3$d$/5$d$ hybrids.
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