Clutch fans can wear out... Then the Fan does not read the temp correctly and will not "lock up" to spin the fan blades. When the Clutch Fan fails it will not pull the correct amount of air and can over heat. There is a test process in the Jeep FSM for the clutch fan. The idea is the clutch slips when you hit the gas and yields quicker rpms and more pep, but when hot the fan clutch does not slip and maxes the cooling.
The lower hose needs to have a spring installed to keep the hose from collasping. You have 2+ year old hoses so they are softer and could be sucked shut at highway speeds and higher rpm running,,,, just the wrong time to suck closed when you need cooling. For this reason, your post on hwy overheating, I think this is part of most of the issue.
The 3 core is thicker than the 2 core. I have the 3 core in a 78 and fits fine. So that could be an option for you.
Inspect the radiator.... if the top of cores are blocked with mineral deposits then there is limited water flow. This is why it is suggested you use distilled water and antifreeze in the radiator. We have hard water here in MN and every house has a watersoftner. YOU SHOULD ALWAYS use distilled water in radiators. The top of the verticle flow tubes is one of the locations the radiator likes to plug with minerals and cuts down your water/collant flow.
I have read.... The water pumps are two styles the std and the reverse flow for the serpentine belt. The inlet hose is mounted in different spots on the water pump and should be able to tell that way. Also the flow should be comming away from the top inlet hose with the cap off.
MY VOTE is your bottom hose is collasping and you may have mineral deposits. The problem in the first set up the clutch fan was worn out and not cooling properly.