I don't see a reason why that wouldn't work, but you will want to manipulate the width or maybe even the height so that you get the right internal air space for the JL.
How come you can't just measure the available space you have in your truck? Figuring the bottom depth is probably the only hard part, but fold the seat down and start measuring and you'll know exactly what you have for space, incase you need to modify the dimensions of the factory box so you have the right airspace for the JL.