"To overhaul the system" means to make major changes or improvements to a particular system, usually to fix its flaws or make it work more effectively. Full definition
What we DO need is to overhaul our system of grain subsidies that is the underpinning of cheap food. (thelunchtray.com)
In Louisiana, education superintendent John White, a former top education official under Bloomberg, has «largely gotten rid of tenure,» he said, and has overhauled its system for teacher evaluations, in conjunction with changes to its curriculum — making it the focus of the national school - choice cause and an envy of New York's reformers. (politico.com)