I just took my '08 JKU (hardtop) out in the desert (rockyhills) to do some shooting and did some good "TWEAKS"--
No SQUEAKS from the hardtop, just some noise from the drivers latch assembly
Having a longer wheelbase, I probably got a little more body flex than that '07 you drove !!
Check the tub torx's and the "T" top rear thumbscrews, probably just a little loose somewhere !!
Good luck !