In idiopathic pulmonary fibrosis (IPF), progressive extracellular matrix (ECM) stiffening and dysregulated levels of growth factors, such as vascular endothelial growth factor A (VEGF-A), disrupt endothelial cell (EC) to pericyte cell communication. The physical coupling of ECs with pericytes in the microcirculation is necessary for maintaining microvessel homeostasis and function, and their uncoupling can lead to both angiogenesis and microvessel regression, the two main processes that dictate microvessel density and tissue perfusion. However, the effects of EC-pericyte uncoupling on microvascular homeostasis in IPF have not been thoroughly investigated, despite the fact that microvessel homeostasis is necessary for lung capillaries to perform their critical role of facilitating gas exchange for the body. Understanding how dysregulated biochemical and biomechanical signals impact EC-pericyte coupling in IPF necessitates the use of a computational model where the effects of these signals can be explored both in isolation and in combination. In this work, we present a multi-scale computational model that integrates EC and pericyte intracellular signaling networks, represented by logic-based network models, with a multi-cell, agent-based model of the IPF lung microenvironment. We used the multi-scale computational model to investigate how combinations of biomechanical and biochemical cues regulate microvascular remodeling. Our multi-scale computational model predicted that ECM stiffness decreased vessel area which was associated with a reduction of EC-pericyte coupling in mature fibrosis (20 kPa). The loss of vessel area and EC-pericyte coupling was exacerbated by nintedanib, an FDA-approved drug for treating IPF, which decreased pericyte quiescence and potentiated pericyte-myofibroblast transition (PMT) in ECM stiffnesses of both 10 and 20 kPa. Finally, we used the multi-scale model to determine that treatment with a YAP/TAZ inhibitor may help to overcome the deleterious effects of nintedanib on EC-pericyte coupling by promoting pericyte quiescence and maintaining microvessel homeostasis.