I have used CLR on both the TJ and XJ that i have with good results....i have had the TYPICAL Jeep heater core problems with both of them.
The way i done mine was to fill the core and lines full of CLR, let it sit for 15 minutes and then FLUSH...i alternated the flow in both directions, forward and reverse until ALL of the derbies came out. I ran it into a white 5 gallon bucket that way i could see when the derbies and sediment stopped coming out of the system.
And this will take a while.
I filled the core up twice with CLR just to get it good and clean, also I was told not to let the CLR sit to long time in the AL core though....after the heater core was clean I then moved to the Radiator, flushing it in both directions...flushed the system with Distilled water then replaced Thermostat and new 50/50 coolant...it's a lengthy process but it seemed to work for me.