The aim of the present study is to analyze the effect of the neutral beam current drive (NBCD), thermal plasma density, and NBI operational regime on the stability of pressure gradient-driven modes (PGDM) and Alfvén eigenmodes (AE) in LHD inward-shifted configurations. The stabilization of n/m=1/2 PGDM (n toroidal mode and m poloidal mode) is observed in the discharge 167 800 during the co-NBCD phase. The iota profile evolution measured by motional stark effect diagnostic may indicate the iota profile up-shift caused by the co-NBCD can induce a non-resonant transition of the rational surface 1/2 before the mode stabilization. The evolution of the iota profile and continuum gaps in the discharge 167 805 during the ctr-NBCD phase leads to the stabilization of the AE, caused by the narrowing of the continuum gap as the iota profile down-shift. Opposite stability trends are identified for PGDM and AE stability with respect to the thermal plasma density. A larger thermal plasma density (larger thermal β) further enhances PGDM although the continuum gaps are narrower leading to configurations with stable AEs. The linear stability of AEs is analyzed using the gyro-fluid FAR3d code to reproduce the AE stability trends observed in the experiments with respect to the NBCD and thermal plasma density. The analysis of hypothetical scenarios dedicated to study different NBI operational regimes with respect to EP energy, and β and radial density profiles indicate off-axis NBI operation shows a higher EP β threshold to destabilize AEs compared to on-axis configuration. This is explained by the presence of a TAE gap in the inner plasma region, easily destabilized by an on-axis NBI injection. The control of the NBCD and thermal plasma in the discharge 167 800 shows a transitory stabilization of PGDM and AEs, as well as an improved discharge performance identified by an increment of the neutron fluxes.