Experiments on the DIII-D tokamak have identified how multiple simultaneous Alfvén eigenmodes (AEs) lead to overlapping wave-particle resonances and stochastic fast-ion transport in fusion grade plasmas [C. S. Collins et al., Phys. Rev. Lett. 116, 095001 (2016)]. The behavior results in a sudden increase in fast-ion transport at a threshold that is well above the linear stability threshold for Alfvén instability. A novel beam modulation technique [W. W. Heidbrink et al., Nucl. Fusion 56, 112011 (2016)], in conjunction with an array of fast-ion diagnostics, probes the transport by measuring the fast-ion flux in different phase-space volumes. Well above the threshold, simulations that utilize the measured mode amplitudes and structures predict a hollow fast-ion profile that resembles the profile measured by fast-ion Dα spectroscopy; the modelling also successfully reproduces the temporal response of neutral-particle signals to beam modulation. The use of different modulated sources probes the details of phase-space transport by populating different regions in phase space and by altering the amplitude of the AEs. Both effects modulate the phase-space flows.