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 130k+ miles. 245-70-17 GG AT2's. BDS 2" lift, Bilstein 5100's, JKS QDs. Addco Swaybars F/R. Stillen Front Rotors/ Pads. TRE's, BJ's, wheel bearings. 100% Amsoil. I like my rifles like my coffee, hot, black and continually refilled.