IMO it's a great thing that replacement rads now come with the trans cooler included. Gives you the option of adding the in-radiator transmission cooling to the stand-alone cooler the KJ came with from the factory. If you don't want the trans cooler lines in the radiator just leave the plastic plugs in the fittings.
Here's how I upgraded my KJ to HD cooling.
Pretty simple process and adding the in-radiator transmission cooler prevents the trans fluid temp from spiking while wheeling or towing.
My 2 cents...
2003 Renegade, Black
- 3.7L, 42RLE, 4X Guard Trans skid, Factory Engine, T-case, Tank skids, Modded BoulderBars sliders, OME 927/948, Bilsteins, JBA A-Arms & 1/4" top plate, 2-ring clevis, 1 extra rear iso/side, Moabs with Firestone Destination AT's 255/70-16. Future: 4.10's