It sounds wierd but, I think it was because I had too long of body posts in the rear. It only bent near the "Arm" or "shoulder" of the tower. (Where the Body posts go). And not badly bent, just enough for the body to not line up correctly. I have a bug body, so the roof is round and then having the posts sticking up too high, they caught the ground when I would slide on the lid...
Problem solved itself, Posts shaved themselves down to sit flush with the body.

The Body just kind of snaps into place and I dont need rear body clips anymore!