OUCH! Well I know mine was rolled with the hard top and the stock cage in it before I got it. I found this out after I bought it though because it was covered in bed liner and you couldn't see it till after the bed liner was off. You are going to have to check the body to see if one side or both didn't shift left or right. You are going to need several straight edges to check things, a sheet rock T square is good to have. Inspect the wheel wells on the inside of the truck one or both might be folded left or right. Check the rear of them too as you might now have a sag at the back of the body.
All of this is pretty easy to fix as you just need a way to get the weight of the truck hanging from the body, a BFH, a 4x4 of wood, and a port-o-power. And when you put in a full cage, make sure you tie it to the frame so that the body doesn't get hosed again.