Plasma rotation plays an important role in the suppression of turbulence, leading to an increase in energy and particle confinement. Significant rotation also leads to a stabilisation of the resistive wall mode. The external momentum input from Neutral Beam Injection (NBI) in current generation fusion plasmas may not be available for future self-heated fusion reactors. Therefore it is important to analyse the phenomenon of spontaneous rotation. At NIFS plasma rotation and momentum transport of the Large Helical Device (LHD) plasma is analysed using a code suite called TASK3D-a. In this work neoclassical effects, which can be especially significant in non-axisymmetric plasmas, were implemented in TASK3D-a. Initial analysis of neoclassical radial momentum flux profiles shows that in NBI-driven momentum input neoclassical effects, especially neoclassical damping, become dominant in the non-center plasma region. It was also found that during and after pellet-injection the neoclassical damping force becomes strong. With the implementation of neoclassical effects new features can be examined in the momentum flux-gradient relations; in the damping-dominated situation following pellet injection a large excursion in momentum flux is found. This work can aid in the search for neoclassical transport-optimised configurations for enhanced (spontaneous) plasma rotation.