If you have a vaild contract for work then the car is NOT abandoned no matter how long they have it.

If the roof leaked because of something NOT included in the accident you may not have any legal stance for a lawsuit against the body shop. Unless they have it in writing that the car needed to be covered if left outdoors, all they have to do is say that they didnt know it needed to be covered and that they moved it indoors as soon as they were told about it.