Additive manufacturing of PEEK/regolith composites offers a promising route for lunar in-space manufacturing by reducing dependence on Earth-supplied materials. However, the processability of these composites and the elastic response of printed components are strongly influenced by regolith loading and manufacturing-induced defects. This study develops a hierarchical finite element framework to quantify the stiffness of additively manufactured PEEK containing 10-50 wt% LMS-1D lunar regolith simulant and to distinguish intrinsic composition effects from defect-driven stiffness losses. The approach combines composition-based estimation of regolith properties with microstructure-informed simulations of PEEK/regolith composites. Under defect-free assumptions, the predicted modulus increases monotonically from 1.27 GPa at 10 wt% to 1.97 GPa at 50 wt%, showing good agreement with experimental trends up to 40 wt%, where deviations remain within 3.5-10.1%. At 50 wt%, however, the experimental modulus decreases to 1.27 GPa, while the defect-free model predicts 1.97 GPa. Microscopy-informed single-layer analyses indicate that tall crack-like interfacial voids, polymer-starved welds, and interconnected weak seams significantly reduce load transfer and shift the mechanical response toward an interface-controlled regime. These results show that regolith additions can enhance stiffness only until defect connectivity becomes dominant. The findings provide insight into the process-structure-property relationships governing ceramic particle-reinforced high-performance thermoplastics in additive manufacturing.