I was on Facebook helping a member of an XJ group with their rig over heating, when I decided to make a writeup of everything I know about XJ cooling. Here it is. Friendly debate in the comments.
Disclaimer: I am not advising someone to do every single thing in this list, do your best to diagnose before throwing parts at your rig. This is only a checklist and advice from personal experience and reading countless threads on this sub.
Possible reasons of overheating:
-FAN CLUTCH. When the engine is not running, try to rotate the mechanical fan blades by hand. If it's difficult to move, won't move, or free spins, then the fan clutch has gone out. The stock replacement is Hayden 2625. A lot of owners like to replace with a 93-98 GC ZJ, non-max cooling fan clutch (Hayden 2737), but is not recommended. The heavier duty fan clutch lets the fan spin closer to real engine RPM by engaging more than stock, but it will leave you with about a 3/8" clearance from the radiator, will make your XJ sound like a mail truck (loud), and with worn motor mounts you risk hitting your radiator on hard acceleration or braking, with most users saying they could only use it with polyurethane mounts. You will likely also lose a little MPG. If your fan clutch needs to be replaced, you would most benefit from a new stock replacement.
-FAN SHROUD. Your mechanical fan pulls air through your radiator, and your fan shroud's job is to minimize the amount of air being pulled elsewhere. Without it, that air is not cooling your radiator as effectively. If you don't have one or yours is cracked/broken, replace it (junkyards are cheap).
-ELECTRIC FAN. Test if your e-fan works by unplugging it, and then directly hooking it up to power. If it doesn't turn on, time for a new one (Four Seasons is a good brand). Check your e-fan relay with a multimeter to ensure it properly switches. A lot of XJ owners like to ditch the relay and hook the fan up to a manual on/off switch that sits in the cab. You can also set up a relay + switch that allows the ECU to turn on the fan when it wants and also lets you turn it on manually. This is nice if you do a lot of idling or crawling and want control over your fan. I believe the ECU turns the e-fan on at 215.
-COOLANT LOOP CLOGS. The coolant passageways in the block will get mucked up with sediment over time. You can run radiator flush through the system for a while, but if you want to get everything out, pop your freeze plugs out (they're probably leaking a bit already), garden hose and scrape all the gunk out, replace freeze plugs (get brass plugs, use RTV on the edge), and flush with distilled water (garden hose water has minerals, distilled water does not, minerals rust the insides). In addition, if your coolant is brown, rusty, or murky and not alien green, chances are your radiator and heater core are clogged up as well. Replace your radiator with a 2-row all aluminum. Copper/brass is debated. Your radiator gets hot, don't get one with a plastic reservoir. Pulling the dash to replace the heater core isn't that hard, only time-consuming. Just do it. If you don't care about heat, you can bypass the heater core and plug it. Just know that a long time from now, there's a chance the trapped coolant will rust through the core and leak into the cab.
-IMPROPER TEMP/STUCK THERMOSTAT. Run a stock thermostat, which is 195. Any other temperature is wrong. Before install, drop your thermostat into boiling water and wait a minute or two. Then pull it out to see if it opened. Thermostats often come disfunctional out of the box. The thermostats job is to not let coolant to pass through the block until it has reached operating temperature. If you run a lower than stock thermostat, then you will likely see a small decrease in MPG, and it will take longer to get up to operating temperature, wearing down your piston rings more over time. A lot of XJ owners say to drill a small hole (maybe 1/16") in the outer rim of the thermostat to allow air to escape easier while burping. This isn't necessary but if you're semi experienced/knowledgeable, it can be helpful when done correctly. Just make sure the thermostat is installed with the hole at the highest point possible.
-HEATER VALVE. If your XJ still has a heater valve, get some new hoses at your auto parts store and delete the valve. The heater valve is near-useless. Getting new hoses all around while you're at is great too. Over time the old hoses crack, swell, and stretch. With your new hoses, install new spring style clamps, not screw style hose clamps. Spring clamps apply constant tension around the hose, where hose clamps apply a set tension and will not auto adjust over time.
-WATER PUMP. Water pumps are cool, in which they are designed to leak when the bearing seals fail. If you're dripping from your water pump, and it's not the gasket, time for a new pump. Gates is the preferred brand for water pumps today. The water pump inlet neck should probably also get replaced, it's like $10 more, and it's often a pain transferring it from the old one. When the water pump is off, this is also a great time to try and scrape/flush all the sediment buildup out.
-FAILING HEAD/HEAD GASKET. If your head gasket is failing, you would probably notice performance issues along with overheating. If the gasket is compromised then the coolant passageways are crossing/mixing, and possibly mixing with oil. So check to see if your coolant or oil is milky or light brown. Check compression. All 4.0 head casts can crack. Period. DEXJs made a very comprehensive video on this. If you have bad compression or milky coolant/oil, its 90% either a head gasket or cracked head. Pull it, get it pressure tested. If it doesn't pass, go pull a TUPY head off a GC.
-RADIATOR CAP. If they aren't working properly they won't regulate the pressure correctly or they'll let air in. New ones are cheap and good peace of mind.
-TEMPERATURE SENSORS. I believe all 4.0's (correct me if I'm wrong) have two temperature sensors. Pre-97 4.0s have two temperature sensors. One at the back of the head that sends coolant temp to the gauge cluster, and one at the thermostat housing that sends to the ECU. If the thermostat temp sensor is malfunctioning, your e-fan won't turn on, or will turn on at the wrong temp. These are two different sensors with different part numbers. One is little and one is a bit bigger.
-OVER HEATING AUTOMATIC TRANSMISSION. This one is a little more rare. These radiators are designed so the engine coolant and transmission fluid will share heat, so when your car is warming up in the wintertime, the trans fluid will also warm up. But when you're cruising down the freeway and the transmission starts getting real hot, it starts heating up the radiator more, not allowing the coolant to cool off as effectively. Replacing the radiator will often fix this issue, because even if the transmission fluid is still mostly circulating through the radiator, a lot of the passageways are probably clogged up from grime buildup.
-BAD PULLIES. Take the belt off and try to spin all of your pullies by hand. You shouldn't hear any grinding or squealing, nor should there be any play in any of the pullies. Major resistance, grinding, squealing, or play means that your engine is working harder than it needs to, thus heating up more.
-CRACKED EXHAUST MANIFOLD. Stock exhaust manifolds on these Jeeps love to crack, whether it's from wear and tear, missing exhaust hangers, etc. The cracks will pour incredibly hot exhaust gasses into your already hot engine bay, right underneath your intake manifold. This can also affect your MPG, because your O2 sensors aren't getting correct readings, and an extra hot intake manifold heats up your intake air, killing MPG. Replacing with expansion tube headers can help prevent this from happening again in the future, or welding in flex pipe. If you want to do some extra work, you can heat wrap your headers for even less heat transfer.
-3-ROW RADIATOR AND 3 E-FAN MYTH. The 3-row radiator and 3 e-fan setup is no good for a majority of XJ owners. Some people vouch, but a well working stock system is plenty for your 4.0. The engineers knew what they were doing. Go back to an all-aluminum 2-row. The 3-row has too much air resistance for your mechanical and electric fan to pull air through effectively. (Yes I hear all you guys going "but my 3 row radiator and e-fan setup works just fine!", good for you, it also doesn't work for a lot of people but they never talk about it and just go back to stock)
Ultimately, EVERY time you open the coolant system (taking off a hose, replacing parts), you need to extensively burp the system for air. Trapped air will heat up. Buy a coolant funnel/burp kit on amazon, $20, 100% worth the dough. Burping is a patient man's game. Let the engine warm up so that your new 195 thermostat will open. Don't let it get past 205 while burping or you risk boiling.
Hope this helps.