We present a novel {em ab initio} approach for computing intramolecular charge and energy transfer rates based upon a projection operator scheme that parses out specific internal nuclear motions that accompany the electronic transition. Our approach concentrates the coupling between the electronic and nuclear degrees of freedom into a small number of reduced harmonic modes that can be written as linear combinations of the vibrational normal modes of the molecular system about a given electronic minima. Using a time-convolutionless master-equation approach, parameterized by accurate quantum-chemical methods, we benchmark the approach against experimental results and predictions from Marcus theory for triplet energy transfer for a series of donor-bridge-acceptor systems. We find that using only a single reduced mode--termed the primary mode, one obtains an accurate evaluation of the golden-rule rate constant and insight into the nuclear motions responsible for coupling the initial and final electronic states. We demonstrate the utility of the approach by computing the inelastic electronic transition rates in a model donor-bridge-acceptor complex that has been experimentally shown that its exciton transfer pathway can be radically modified by mode-specific infrared excitation of its vibrational mode.