To achieve high-fidelity operations on a large-scale quantum computer, the parameters of the physical system must be efficiently characterized with high accuracy. For trapped ions, the entanglement between qubits are mediated by the motional modes of the ion chain, and thus characterizing the motional-mode parameters becomes essential. In this paper, we develop and explore physical models that accurately predict both magnitude and sign of the Lamb-Dicke parameters when the modes are probed in parallel. We further devise an advanced characterization protocol that shortens the characterization time by more than an order of magnitude, when compared to that of the conventional method that only uses mode spectroscopy. We discuss potential ramifications of our results to the development of a scalable trapped-ion quantum computer, viewed through the lens of system-level resource trade offs.