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We introduce a two-step simulation methodology that is used to engineer a typical avionics telecommunication system based on step-index plastic optical fiber (SI-POF). The approach combines a phenomenological model that solves the spatial propagation equation in SI-POF and optical connectors and a time/frequency-domain approach using a commercial simulation tool. SI-POF as well as connectors are characterized using the experiment and a system case study is engineered using the above model. This approach provides a faster and more efficient modeling methodology compared to using the traditional time/frequency-domain approach.