I'm confused because you said you replaced the fan clutch and you also say you have an electronic fan.
Which is it?

 

Both my man, they sit side by side behind the radiator

 

Hm. To be honest, I'm not familiar with that setup, I have a 98 xj out in the garage, I will have to go look. Oh, ok, this is happening on an '01, got it. That said, if you don't have a leaky head gasket and Since it manifests at stop signs, that has the hallmark of a cooling fan problem. Are you sure the electric fan(s) are working? Are they blades spinning the right direction? And, is the pump pumping? Fan clutch was squealing like a pig you said, are you sure it wasn't the pump that was squealing, and even if it was the fan clutch squealing, that would still make the pump suspect as the pump drives the clutch fan? Are the electric thermostats working at the right temp? Replace? Hope this helps.

 

The electric fan in working fine. And the belt driven fan is not connected to the water pump it's connected to another pully
Also I found out that the previous owner had already replaced the pump.

 

Youve got a blockage somewhere. Flush your heater core. Replace your fan clutch and upgrade to the zj clutch. Are you running a proper 50/50 mix of Distilled Water and raw coolant? It took me 4 flushes to get all the crud cleaned out of my radiator and heater core. Make sure your serpentine belt is properly tightened. if it is loose, it will slip on the pump pulley causing an overheat.

 

How do you know? Did he tell you or show you receipts? My origional pump looked new untl i opened up and looked at the rotor.

 

Pulled it out to check it. The pump is not the one from the factory that they used. It's an aftermarket. I could tell from the serial number and company name on he pump.

 

Already flushed the heater core and back flushed the system 3 times now. Everything is clear. The fan clutch was replaced last week by me.
The belt is tight. Everything except for the water pump has been replaced.

 

Temp sending unit or gauge? Sounds like everything else is replaced.

 

That's what I thought at first too. But I just opened the system yesterday to put a lower temp thermostat in so I think there might be an air bubble in there still

 

Im just spitting out something, might not be it,, but hell.. How is your AC condenser? does it looked all plug up and smashed not allowing good air flow.

 

When I replaced the radiator I checked it. Looks fine no dings dents or bent fins

 

Can you see the coolant flowing, or verify it? maybe pull a heater hose, let it heat up till the thermo opens and it should run like crazy...
"the previous owner replaced my fuel pump too" ...that is why I had to replace it. The fact that you say you can cool it off by revving it might mean you have some kind of pump action, but I have heard of wrong pumps with the opposite push...and of course broken impellers, can you see the electric fans kick on at idle?

 

The e-fan foes kick on. And I can verify coolant flow. If I remove the radiator cap I can see it flowing out as the thermostat opens up

 

Well, this is a good one. Hmm. If you have circulation, and fans, then you should have cooling. Pull the sender and check it? If you have a scan tool, what is the temp of the coolant temp sender at? This is not the same as the sender for the dash temp and will independently verify what the dash is saying. Pressure test the cooling system and the cap?