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A possibility is the water pump. This is what circulates the water through the engine and back to the radiator for cooling. Water pumps consist of several vanes attached to a rotating shaft. If a few vanes are broken, you'll get reduced water circulation, causing overheating.
sounds like you have blown the internal heater matrix and the thermostat is not working or is blocked. you are going to need a new matrix and thermostat and a bloody good flush out of the system just in case there is something in the system means taking off the rad hoses flush them out from both ends. and doing the same to the engine. replacing the matrix as its not going to be able to fix it if its shooting water out of the vents change the thermostat check pipes for damage.
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.
Did you make sure you filled the radiator up and got the overflow tank up to the correct level? Sometimes when you flush and drain the system and fill it back up air pockets can get trapped in the system. Start the jeep up with the radiator cap off and wait for the coolant to start flowing and when the air pockets make their way through they will escape and you can add more antifreeze.
Also, did you make sure you installed the thermostat so it is facing the right direction?
There may be coolant in the reservior but it doesn't necessarily mean there's any or enough in the main cooling system. If the radiator has a pressure cap, try replacing it with a known good one. Check and replace any coolant hoses that are kinked, or collapsed. There may be an airlock in the system - bleed it in accordance with the manufacturers instructions. Try flushing out the radiator and cooling system and then refill with the appropriate antifreeze / water mix ensuring that no air locks remain.
You say you changed the fan relay and the thermostat? when was the last time you had the cooling system flushed? you could have a blockage in your cooling system that could be keeping the coolant from circulating..