Just in case this helps someone else. I recently bought a 2006 T4R Limited (mods in process: FJ Springs and Shocks, FJ Wheels, 2/1 Cornfed lift). I had a super annoying rattle that would come and go. It sounded like a loose hubcap or something like that. It sounded like it was coming from the running board and since I planned in ditching them anyway I took them off but this didn't help. I checked every nut and bolt looking for something loose but found nothing. Yesterday I moved my head around in the cab while it was rattling loudly and when my head was in a certain place it sounded like it was coming from the roof. When I stopped I checked the locks in the roof rack and they were all tight but the cross member was loose in its slots. I simply loosened the locks on one side (front and back) and slid the cross member forward until there was some good tension then I tightened the locks while under tension from skewing the cross member. Long story short, rattle gone! This bugged me for a long time so I hope it helps somebody.