When discussing the two types of cooling systems the XJ uses, the terms "open" and "closed" are actually reversed, but have come to be accepted that way among the XJ community, so in this article I will hold to them to avoid confusion.  The "closed" system refers to the one that uses a pressure (or expansion) bottle which is at the same pressure as the system, unlike the "open" system which uses a conventional radiator cap and coolant recovery bottle that is not under system pressure.  One other point I will make that is not common knowledge, is the plastic coolant cap on the pressure bottle has a pressure relief valve built into it, so it is  a pressure cap, even though it doesn't appear to be.  There are slots in the threads of the cap to allow excess coolant and pressure to escape when the cap is screwed on.

    The closed system needs to stay "closed" in order to function properly.  As long as the system is under pressure, and there is no (or very little) air in it, it can tolerate temps above boiling, and continue to maintain normal operation.  However as soon as any leak develops (crack in the bottle, defective cap, loose hose clamp, etc.), pressure is lost and the coolant starts to boil.  Once the boiling starts, coolant is pushed out through the pressure cap, and unlike an "open" system, there is no way to recover the lost coolant, so it is replaced by air as the engine cools down. Once this happens, overheating is inevitable.  Everything has to be in perfect order for it to operate normally.

    There are a couple of weak points in the system.  The first is the coolant bottle.  Its plastic and does not hold up well to the extreme temps and pressures encountered in the 4.0 system.  It cracks easily, usually around the bottom hose outlet.  Also the mating surface of the filler neck/cap can become slightly distorted and prevent a good seal.  The plastic cap itself is inherently weak and is also prone to failure.  The most common failure I have encountered with the cap is the seal (the flat "O" ring) inside.  Over time it becomes distorted and allows pressure to escape, leading to overheating.  Also it is easy to tighten the cap too much, forcing the seal out of place and allowing it to leak.  I found I got a very short life from the cap and had to replace it often.  I highly recommend carrying a spare since they are not available from just any old auto parts store, and it's usually way out in the "boonies" when it starts to leak.  This is cheap insurance.

    After flushing the system, or replacing any component of it (or after an overheating episode resulting in coolant loss), it is necessary to bleed the air from the system so it will operate properly.  Under normal circumstances, it might eventually "burp" itself, however usually not without an overheating episode or two.
 

In order to bleed the air from the system do, the following:

It is best if you jack up the rear of the vehicle in order to raise the back of the engine (this is optional, but provides a more complete purging).  With the engine off, fill the system until the coolant bottle is topped off, leave the cap off and using a 13mm deep socket, unscrew the coolant temp sensor (located on the top of the cylinder head at the rear on the driver's side), and slowly start to pull it out until you hear air escaping (you don't have to pull it all the way out, it extends down beyond the threads), coolant will soon follow, at which point you screw the sensor back in and tighten it snugly. Now top off the coolant bottle if necessary, and install the cap.  When the engine reaches operating temperature, the excess coolant will be forced out through the pressure cap as the system stabilizes itself.  This is a normal process so don't be alarmed by the escaping coolant.
 
 

>> Warning! <<

Never, ever unscrew the temp sender with the engine running, or start it up with the sender loose in its threads! (Not even on a cold engine).  It will be launched into orbit, and you will be left standing there covered in coolant, wondering where you will find another one late Saturday afternoon }:o<
(please refrain from asking how I know this!)
 

Other Cooling Tidbits

    There is a popular misconception that installing a lower temp thermostat will help an engine run cooler, and/or solve an overheating problem.  This is simply not true.  The engine will still operate at the same temp regardless of what thermostat you install.  The only function of the thermostat is to determine at what temperature the coolant starts to circulate through the system.  It does not determine how hot the engine can get after it opens.  That is a function of the system's capacity and radiator's ability to exchange or dissipate heat.  Once the thermostat opens (whether it's at 195º, 180º, or 160º) the coolant starts to flow and the engine will eventually heat the system to the same temperature, it will just take a little longer with a lower temp thermostat opening sooner, and this is not what you want.  Since the internal combustion engine is less efficient at sub-normal operating temps, the thermostat is designed to get the engine temperature up to normal as soon as possible.  By installing a low temp thermostat, you are probably doing more harm than good.  Another popular "Band-Aid" fix is a high flow thermostat and housing.  This will help some, but is seldom enough to solve the inherent overheating problems of the early 4.0.  Increasing flow does not always improve a cooling system's ability to cool an engine.  This is why it is never recommended to remove the thermostat completely.  Flow can be increased to the point where the heat doesn't have time to transfer, and in many cases can make things worse.  For this reason a high flow water pump will not necessarily help either, unless the original design was too restrictive to begin with, which is not the case with the 4.0.  Remember the warning about the temp sensor being launched into orbit?  A stock 4.0 water pump can produce enough pressure and flow to blow the sensor out of its hole.  The key to cooling is heat transfer.  This is a function of coolant capacity and heat dissipation, not just the speed of the circulating coolant.  It is the ability of the coolant to collect as much heat as possible while it is in the engine, then dissipate it in the radiator.  The radiator is the prime component in this process and it needs to lower the temperature of the coolant as much as possible before it is pumped back into the engine.  Since the coolant capacity of the engine itself cannot be increased, the radiator is the likely candidate for improvement.  The 4.0 radiator was under designed from the beginning and is marginal at best.  Even in perfect condition it is only adequate, and there is no margin for extreme (or even moderate) conditions.  If you are having overheating problems (or just want to insure you don't), you need to increase the efficiency of the cooling system by either increasing its capacity, or increasing its ability to transfer and dissipate heat.  An aftermarket radiator will do both.  A 3-row radiator increases the capacity of the cooling system and exposes more coolant to the airflow at the same time.
 

    Even the Jeep engineers admit the "closed" system was the worst mistake Jeep ever made, and in mid '91 it was dumped in favor of a conventional recovery style system.  Unfortunately they did not improve the radiator much, but adding a filler neck with a conventional metal pressure cap and a coolant recovery bottle was a giant step in the right direction.  If you are interested in eliminating all the idiosyncrasies of the "closed" system once and for all, consider converting your current system to the later style "open" system.  All the components are a direct replacement and no modifications are required.  It is well worth the $200+, especially if you tow a trailer, live in a warm climate, or are planning on having your radiator internally cleaned by a shop.

Here are some links to other articles I have written related to the cooling (and heating) of the XJ.

Converting to the newer style "Open Cooling System"

Why the Auxiliary Fan doesn't come on
until the engine is already overheating

Auxiliary Cooling fan Manual Override Switch

Heater Core Flushing Made EZ
 

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