We present a combined experimental and theoretical study of the spectrum of magnetically tunable Feshbach resonances in NaLi (a 3 Σ + ) + Na collisions. In the accompanying paper, we observe experimentally 8 and 17 resonances occur between B = 0 and 1400 G in upper and lower spinstretched states, respectively. Here, we perform ab initio calculations of the NaLi + Na interaction potential and describe in detail the coupled-channel scattering calculations of the Feshbach resonance spectrum. The positions of the resonances cannot be predicted with realistic uncertainty in the state-of-the-art ab initio potential, but our calculations yield a typical number of resonances that is in near-quantitative agreement with experiment. We show that the main coupling mechanism results from spin-rotation and spin-spin couplings in combination with the anisotropic atom-molecule interaction. The calculations furthermore explain the qualitative difference between the numbers of resonances in either spin state.