Had this problem and one thing that even Chilton manuals only show in fine print sorta say is that Jeep cherokee has a relay sensor for the coolant fan usualy right behind the passenger or driver side headlight you may have to remove the bumper also its rather easy.Its a liitle black box thats screwd down on the panel just unscrew it unplug it replace mine ran me around $60.00.Before I learned about this after replacing the thermostate and just about to rip out the water pump my buddy told me about the sensor after replacing over a year ago no problems.
Have you "burped" the cooling system? I had the same issue. My fan always came on. Make sure you have your connections on tight.
To "burp" the system: (Jeep should be cool when atempting this)
Have 1 to 2 gallons of 50/50 antifreeze ready with running water from a water hose.
Park the car on an incline. (driveway or something simular)
Remove the radiator cap.
Start your Jeep with the radiator cap off
Turn on A/C with RECIRC and full heat.
Wait for Jeep to warm up to normal operating temps.
Once the jeep heats up, the thermostat should open allowing coolant levels to drop. This means that the thermostat is working. Air or bubbles should take place of the coolant lost. Top off the coolant in the radiator until coolant overflows from the radiator spout. Keep doing this until no more air or bubbles come from the radiator. This should solve your problem.
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If you have a viscous fan hub then have it replaced as it is not drawing air through the radiator at idle or slow speed (crawling traffic). Check that are no air locks in the system as they will cause heating problems.
Heating up while idling for long periods is normal, so is cooling a little when accelerating as the water pump is moving the water a bit faster. As long as it drops to normal temp when in normal use it is ok, if it overheats either your thermostat is faulty or your electric fan is not coming on when it should. Does the elecrtic fan ever come on?
Good chance your radiator is partially obstructed internally or externally (check front of condenser for bugs leaves etc and between condenser and radiator for same). 4.0's tend to internally rust and send rust particles into the radiator core. The radiator itself is actually smaller than it should be and therefore very sensitive to obstructions, Sometimes flushing with a good chem cleaner will help other times, you need to have a radiator shop do that. After doing the normal flush, disconnect the radiator from the engine entirely and run water through it in both directions. I generally remove them so it can be turned on it's end so debris can fall out while doing that. Assuming that you see no white smoke from the tailpipe, have installed the thermostat in the right direction (spring towards engine) and have no leaks, that should help. Your fan is controlled by the computer and comes on when the computer sees higher temps. Only time fan should run full time is with a/c on.
Check your radiator for external and internal obstructions (leaves, bugs etc on the a/c condenser or leaves between the condenser and radiator, rust or calcium deposits inside the radiator core all cause loss of heat transfer) Also make sure that the system is full and that the electric fan and the clutch fan are operating properly. (electric fan should come on just above normal operating temp and clutch fan should not be "freewheeling" above temp either) Note: If you need to have the radiator flushed, do it separately from the engine. especially the inline 6 and 4 engines rust up inside and if the system is flushed with the radiator connected, the debris will pack up inside it and actually can worsen the condition.
When the engine is at operating temp check the electric cooling fan. If it is not moving then i would check the fan relay which is located under the right side headlamp. 9 times out of 10 this is the problem