Check that your top isn't too tight on the body. I always back off the hard top slightly so it can shift if need be. Your cage shouldn't be moving at all. If anything the cage should help to stiffen the body from flexing. I've had my hard top on for 1 1/2 years and it does fine everywhere. Just snug it down, so it can float.
One of my LJ Unlimited friends actully cracked his hard top it was on so tight. Right at the back screw, it cracked all the way up the side. Luckly Jeep warrentied the top, and now he doesn't over tighten it anymore
BTW, the Jeep looks great!