In this work, we examine the validity of several common simplifying assumptions used in numerical neoclassical calculations for nonaxisymmetric plasmas, both by using a new continuum drift-kinetic code and by considering analytic properties of the kinetic equation. First, neoclassical phenomena are computed for the LHD and W7-X stellarators using several versions of the drift-kinetic equation, including the commonly used incompressible-E × B-drift approximation and two other variants, corresponding to different effective particle trajectories. It is found that for electric fields below roughly one third of the resonant value, the different formulations give nearly identical results, demonstrating the incompressible E ×B-drift approximation is quite accurate in this regime. However, near the electric field resonance, the models yield substantially different results. We also compare results for various collision operators, including the full linearized Fokker-Planck operator. At low collisionality, the radial transport driven by radial gradients is nearly identical for the different operators, while in other cases it is found to be important that collisions conserve momentum.