When I got my TJ, its cooling system was filled with a brown sludge. I never figured out if it was mostly rust, incompatible coolants mixed together, or some sort of stop leak product. But now having a cooling system with clean coolant, these are the steps I took to tackle the job. First I drained the radiator. This can be done at the little drain on the passenger side, but since that can clog up and/or break, I’d recommend disconnecting the lower radiator hose to drain it.
If what comes out is clean, then the quality of the coolant is probably not your issue. In this case, you’d want to check that the thermostat is working correctly. And if you remove the thermostat housing, you might as well put in a new thermostat since you do not know how old the current one is. You’d also want to check that coolant is flowing properly theough all passages. To do this you can put a garden hose into different components of the cooling system and see if it flows out the other side. You want to be careful not to apply too much pressure into the heater core and/or radiator, especially if they are older or corroded. This may cause a weak spot to burst.
If the first coolant draining shows dirty coolant, then your problem is likely at least partially caused by sediment, rust, and other muck and solids plugging up hoses, the radiator, and the heater core. You do not need the heater core to be clear for the rest of the cooling system to keep the engine cool, but if it is plugged up, then the rest of the system is probably in need of a cleaning too. The first thing I did was to run a hose through the radiator, the heater core, the coolant passages of the engine block, and the coolant overflow tank, all separately, and all until the outflowing water was clear. Note that the thermostat needs to be removed to get water to flow easily through the engine block. And you will need to remove hoses to direct water through each of these components. This will get a ton of the bad stuff out. Then I refilled with water (distilled is recommended when you will be running the motor). Drive it around a little bit either with the thermostat removed or until the thermostat opens up at running temp. Let the engine cool and drain it. I repeated this process several times until it was clean. You could just skip to using a cleaning flush product if you are in a hurry though. Depending on what is plugging your cooling system, different flushes will work better or worse for you. I was unsure, so I started with Irontite thoroflush and water. You can follow the directions or drive around with it in there for a couple days like I did. Then drain and flush it all out with water throroughly. This got all the junk, muck, and gel out, but not all of the rust. For the rust, I used thermocure and water. I drove around with it in my cooling system for a week and it stripped all the rust out. Worked like magic. I should mention that I replaced my radiator after this step, but only because it was looking very old and beat up. I would suggest replacing parts that you notice may need replacing like hoses, thermostat, water pump, etc. if anything isn’t functioning or looks like it may fail soon such as cracked hoses. My heater core started leaking after these flushes, since they stripped all the corroded metal out of it. Neither flush did any harm to any uncorroded metal in the system, however. Once everything is cleaned out and any parts are reolaced if need be, then the system is ready to be refilled with 50% coolant and 50% distilled water.
Basically you just want the system to be clean, with no leaks, have a properly functioning thermostat and fan clutch. Once all those conditions are met, there is no reason the engine should ever overheat. Aside from the heater core, which is mildly irritating to get access to, the rest of the cooling system is very accessible and simple to work on. A couple more tips- if you are replacing the thermostat, make sure you put in a quality brand 195° one, which is what the manual recommends. Some people install one that opens at a cooler temp, but this does not allow the engine to reach the proper temperature for ideal running conditions. Next thing is that you will want to replace the gaskets of the water pump and thermostat housing if you have to remove them, so get those ahead of time. Last thing-if your heater core leaks at any point, you can simply bypass it with a fitting that connects its inflow and outflow hoses together. I did this temporarily until I tackled the heater core replacement.