Shocks will help your ride quality, meaning that if you feel every bump in the road, some new shocks can help to make it a little gentler, but they don't affect the height of your Jeep.
I'm guessing that your wheels are rubbing on the plastic fender flares on your Jeep - is that correct? If thats the case you have a couple of ways to fix it.
1. Trimming your body. This would probably help in back, but not the front of your Jeep. You actually take a saw and cut yourself new wheel wells. You probably don't want to do this.
2. Get a larger suspension lift. Go from 3.5 to something higher. this will get pretty expensive, and is a good amount of work, but will solve your problem.
3. Smaller tires. nahhhh......
4. Get a body lift. This is probably the best solution to your problem. A body lift raises the body of your Jeep (the colored / painted portion) off the frame (the black "skeleton" of your Jeep). This is done by just adding spacers (rubber washers) between your body and frame. Since the body is an inch or two higher, and the frame is the same your wheels (attached to the frame) will have an extra inch or two from the body.
You've got some big tires, and I'm not sure if a 3.5 inch suspension lift, with a 2 inch body lift is enough, but it's a step in the right direction.
http://www.jeepz.com/forum/suspension/16939-body-lift.html
In the picture, imagine the red body mounts as being stock, and the black washer / puck as being a one inch body lift. The highest body lift I'd recommend would be 2" (for safety reasons), but you can find higher.
