If you are planning on keeping your WJ, swap out to Akebonos now. Easy to change out and what an improvement (I did Kolak's Stillen disks/pads).
If you aren't sure you will keep the Jeep, then do a front rotor swap. If that doesn't remove the pulsing, then do rear rotors.
'02 Overland 190k+ miles. 2.5" lift w/springs. All Control Arms upgraded, dual Addco sways.