Interpreting data using mechanistic mathematical models provides a foundation for discovery and decision-making in all areas of science and engineering. Key steps in using mechanistic mathematical models to interpret data include: (i) identifiability analysis; (ii) parameter estimation; and (iii) model prediction. Here we present a systematic, computationally efficient likelihood-based workflow that addresses all three steps in a unified way. Recently developed methods for constructing profile-wise prediction intervals enable this workflow and provide the central linkage between different workflow components. These methods propagate profile-likelihood-based confidence sets for model parameters to predictions in a way that isolates how different parameter combinations affect model predictions. We show how to extend these profile-wise prediction intervals to two-dimensional interest parameters, and then combine profile-wise prediction confidence sets to give an overall prediction confidence set that approximates the full likelihood-based prediction confidence set well.  We apply our methods to a range of synthetic data and real-world ecological data describing re-growth of coral reefs on the Great Barrier Reef after some external disturbance, such as a tropical cyclone or coral bleaching event.