1. Blown Head Gasket: Overheating can cause the head gasket to fail, resulting in compression and coolant leaks. This can cause a rough idle and overheating, and eventually prevent the engine from starting.
2. Warped Cylinder Head: Extreme heat can warp the cylinder head, affecting the engine's compression and causing it to run rough. A warped cylinder head can also lead to coolant leaks and overheating.
3. Cracked Engine Block: In severe overheating cases, the engine block itself can crack, leading to coolant or oil leaks and causing the engine to cease running.
4. Damaged Engine Components: Overheating can damage various engine components such as pistons, rings, and valves, causing the engine to run rough or not start at all.
5. Coolant System Issues: If the radiator flush did not remove all the air pockets or if there are any other issues in the coolant system, such as a faulty thermostat or water pump, it can cause the engine to overheat and run rough.
6. Electrical Issues: Overheating can damage electrical components, such as sensors, wiring, or the starter, preventing the engine from starting.
7. Fuel System Problems: Overheating can affect the fuel system, such as vaporizing the fuel in the lines or causing the fuel injector to malfunction, resulting in a rough idle or starting problems.
8. Computer Issues: The engine control unit (ECU) relies on sensors to monitor and adjust engine functions. If the sensors are damaged or faulty due to overheating, the ECU may not be able to control the engine properly, causing it to run rough or not start.
It is important to address overheating issues as soon as possible to minimize engine damage. Since your Jeep has multiple potential issues, I recommend having it diagnosed by a qualified mechanic who can evaluate the specific cause of the overheating and starting problem and recommend the necessary repairs.