The fibula free flap has been widely used for reconstructing large segmental bone defects in the maxillofacial region. While mandibular reconstruction requires a high degree of precision, the impact of surgical deviations on clinical outcomes remains poorly understood. This study addressed geometric inaccuracies during surgery and examined the effects of loading patterns on the biomechanical behavior of reconstructed mandibles. Patient-specific finite element (FE) models were developed using CT data from three representative cases - two with Brown Class II defects and one with a Class III defect - reconstructed with single, double, and triple fibula segments. The computational analysis results revealed that minimizing the gap between native and grafted bones reduces stress on the reconstruction plate by approximately 30%. When gaps are unavoidable, anterior placement results in the least biomechanical impact, increasing stress by only 6%. To optimize the outcome, alternating ipsilateral and contralateral posterior loading is recommended to ensure adequate contact pressure at the osteotomy site while minimizing the stress on the plate. In addition, incisor loading should be limited to patients with multiple grafted segments to prevent stress concentration on the plate. These in-silico findings provide critical biomechanical insights to refine surgical techniques and develop patient-specific occlusal loading guidelines, ultimately improving long-term outcomes in mandibular reconstruction.