Why is my 03 grand Cherokee overheating?

May have a clogged radiator or cooling ports in engine block try using a good cooling system flush Prestone Super Flush is really good also may want to spray out radiator and A.C condenser coils with a garden hose and nozzle because of partially clogged with dirt and bugs will restrict air flow across coil fins.

I plan on going to the car wash to spray out the fins soon. Did a OK job on flushing the motor as I have no access to a garden hose but made do with a few gallons of water. I replaced the radiator fan connectors with crimps because they were burnt and also replaced the fan relay again (the prongs were burnt must have shorted the relay) and I think it's working fine. What troubles me is I ran it for an hour and my radiator cap is cold while my upper hose is scolding hot... Collapsed hose? Water pump? This is killin me now

Sounds like you have air in the system to bleed follow these directions. Remove cap from over flow tank, fill with anti freeze to full mark leave cap off and start vehicle, let idle and reach operating temp, when thermostat starts to open anti freeze level in over flow tank will drop add more anti freeze to full mark then put cap back on all air should be removed from system unless there is another problem.

Are you sure you did not install the thermostat in the wrong way ? Trust me it is very easy to do

Also you may have gotten hold of a bad new thermostat seen it happen many times. I believe the thermostat is easy to get to on that vehicle remove thermostat and reinstall hose with out thermostat and see if vehicle still overheats.

Propped the front left on a curb and opened the radiator cap and air shot out. Looks like there was a nice air bubble in there. Topped it off and let it run until it stopped sucking antifreeze in. I'm hoping that the new fan relay/crimps and added anti freeze fixes it. Next step is checking the "new thermostat" then water pump. I know I installed it in the right direction but cheap parts are cheap parts.

Thank you by the way for the info. Much appreciated.

Can you confirm if the air bubble was the problem. I have a 03 grand cherokee that's doing the same thing.