Long-period (T > 10 s) shear-wave reverberations between the surface and reflecting boundaries below seismic stations are useful for studying the mantle transition zone (MTZ) but finite-frequency effects may complicate the interpretation of waveform stacks. Using waveform data from the USArray and spectral-element method synthetics for 3-D seismic models, we illustrate that a common-reflection point (CRP) modeling of layering in the upper mantle must be based on 3-D reference structures and accurate calculations of reverberation traveltimes. Our CRP mapping of recorded waveforms places the 410-km and 660-km phase boundaries about 15 km deeper beneath the western US than beneath the central-eastern US if it is based on the 1-D PREM model. The apparent east-to-west deepening of the MTZ disappears in the CRP image if we account for shear-wave velocity variations in the mantle. We also find that ray theory overpredicts the traveltime delays of the reverberations if 3-D velocity variations in the mantle are prescribed by global models S40RTS, SEMUCB-WM1, and TX2015. Undulations of the 410-km and 660-km are underestimated in the analysis when their wavelengths are smaller than the Fresnel zones of the wave reverberations in the MTZ.