im in a 99 . with a 4.5 rustys ,adj lower conrtol arms .adj track bar.. on 31's .. im getting some serious rubing when flexing on the pass side .. accually ripped off the flare and dented behind the tire.. my lca's are set at 16 1/4 in and i mesured (centered ) the track bar when i installed .. the jeep tracks nice on the road . not sure where to start .. no rubbing on the driver side ..
thanks

 

Try adding to your bump stops

 

this is a good place to start, you also might want to trim your fenders
everybodys doing it lol

 

If it's rubbing on one side but not the other (hopefully when subjected to the same type obsticle) then I would start taking measurements and compare the Drivers side to the Passenger side.
Maybe drive up on something to flex the suspension on the drivers side then drive up on it on the passenger side. Get out and take a look at what's going on with the suspension each flex.
This way you may be able to spot something or measure something different side-to-side.
How about posting a picture or two of it flexed on both sides and the damage you experienced on the passenger side. That is the only way we can make an educated guess on what the solution might be.