So, I read through a lot of the audio threads, and SHOBoats was probably the most inspiring, for me.
I'm doing something essentially similar, with a stealth box in the spare tire well, but utilizing a single 12" subwoofer.
The parts being used:
SPL 12" 2600-watt max subwoofer
Planet Audio 3000-watt monoblock Class D amplifier
Audio Control LC2-i line converter
This is my first attempt at any kind of custom enclosure, and I'll probably have to make a second one before this is all done, but I got enough materials to make it happen!! What I'm envisioning is a top firing sealed box with a raised floor frame, to keep the packages in the rear off the woofer and give the trunk a level flat floor surface.
Started with this:



Worked into this:



I drilled the spot welds out of this bracket and popped it out. No more spare tire or jack/tools bolt down capability.

I had some issues with this box, namely the fact that while I calculated my airspace volume correctly, I didn't have the right figure for my speaker. D'OH!! This first enclosure ended up being too tall, so I made a second one, with the right airspace volume specs, so I was able to keep the same width, add 1.5" in length, and lose 3" in height.
Pictures of Enclosure 2.0 are in a post below. I'll follow up with more, as I get there.