Accuracy and reliability are extremely important when computational modeling is used to analyze biological systems and make diagnostic decisions and clinical predictions. Recently we have introduced three-dimensional (3D) MRI-based models with multi-component plaque structure and fluid-structure interactions (FSI) to perform mechanical image analysis for human atherosclerotic plaques and identify critical flow and stress/strain conditions which may be related to plaque rupture. In this paper, further sensitivity analysis is performed to quantify effects of various controlling factors on stress/strain distributions in the plaque. Our results indicate that pressure conditions, plaque structure, component size and location, plaque cap thickness, material properties, and model assumptions all have considerable effects on flow and plaque stress/strain behaviors. Large-scale patient studies are needed to validate computational findings. This FSI multi-component model provides more complete stress/strain analysis and better interpretation of information from MR images and may lead to more accurate plaque vulnerability assessment and rupture predictions.