I doubt that a 5ft kryptonite will fit in the seat. Maybe, but doubt, the chain itself, but not the lock. I have a 3 footer and I just put it in a backpack or keep it locked around the pole I chain my bike to. Last option would be to wrap it around your torso and shoulder.
theres no way you will get it in the "trunk". Plus its too heavy to be stored in there. You can also try wrapping it around the space between your seat and the rear seat, looping it through the passenger pegs. Thats what i did and it worked.