Did a cage this spring. It sandwiches the floor in 8 places, under all 8 points are poly bushings, then tied to the frame. The back of the cab is cut out weakening the body, but then the bed and cab are welded together. There is 0 chassis flex with the cage, otherwise we would be seeing signs at the cab/bed meet points.
No negatives noticed.
Build thread here:
http://www.rme4x4.com/showthread.php?t=80742&highlight=toyota