*UPDATE*
I designed how I'm going to arrange the guts. I'm pretty sure the diagram is completely to scale, as I must of spent half an hour with a ruler just measuring, measuring again, and carefully quadruple checking my measuring. Anyways, the mobo in the picture is upside down for a reason, so that the expansion pak will stick out the back. Also, the memory pak is going to stick out the back. The slot as you can see is right behind the 'Start' button. The reason it is so thin is that only the PCB is going to stick out. Then I'll probably use a small aluminum box to cover up both of them. Anyways, on with the picture, proving that it will all be stuffable (but maybe with a bit of dremeling needed, but nothing that will make it unrecognizable as a Battleship case)
By the way, I had to ditch the D-Pad because of the needed space for batteries. Also, because the image is for my personal usage pretty much only, it is not labeled because I already knew what everything was. So just figure it out yourself. Finally, most of the pics of boards and stuff are courtesy of anotherperson.
Also, I have decided it will either be called the Battleship 64, or B-Ship 64. I was thinking of calling it the 'BS64' but you can probably see the obvious reason not.
Until next time, happy portabalizing, and may the force be with you!

I'd imagine right now you wish you were a cuttlefish...