Congestion in the Emergency Department (ED) is one of the most important issues in healthcare systems. The lack of downstream beds can deteriorate the quality of care for patients who need hospitalization after an ED visit. We propose a generic simulation model in order to analyze patient pathways from the ED to hospital discharge. The model is adaptable for all pathologies and can include several hospitals within a healthcare network. A pathway analysis using Process Mining is done in order to identify relevant pathways. Then we propose several designs of experiments in order to test medical unit capacity variations taking into account real data and practitioners expertise. A practical case study on stroke patient pathways in the Southern Brittany Hospital is proposed to illustrate the approach. Results show that the best way to improve the number of optimal pathways is to increase the capacity of Rehabilitative Care units.