Quality improvement methods such as robust design, statistical process control (SPC), and inspection have received significant attention over the past decade. Despite the plethora of research, there is very little work that describes how to allocate quality control methods in a complex system. This paper focuses on how to choose an inspection plan to remove the most variation at the lowest cost. This paper describes how to quantitatively allocate inspection locations in a complex assembly using a combination of modeling, simulation, and simulated annealing. It demonstrates the functionality of the theory using an example from the aircraft industry. The model provides three improvements over current methods: 1) methods to optimize both inspection limits and inspection locations, 2) the ability to mix both rework and scrap, 3) explicit calculation of the probability distributions for each point in the assembly.