2004 TJ overheating problem

So you didn't replace the fan clutch? I'd say do that. Make sure the selected clutch is for the correct direction of rotation.
 
It's a 3 row radiator, there is but one core. Yours may run fine with a 3 row radiator but the number of rows it has has no direct bearing on how well it will cool. In fact, Jeep went from a 2 row radiator to a 1 row radiator within a year or two of the introduction of the TJ. The new 1 row design had slightly better cooling characteristics. More rows does not mean better cooling.

P.S. The OE Mopar radiator has an all aluminum core.
I went from not being able to run my A/C with out overheating regardless of the ambient temperature to bring able to run it when the ambient temp is 100+.