In doing my research and with what you guys have suggested, I've pretty much convinced myself of option #3.
I've fiberglassed before and created an enclosure in my spare wheel of my other car so glassing is not a problem.
My current approach is to make a custom enclosure in the stock location out of fiberglass and mdf. From there, I am torn between two ideas:
1) Run an inverted 10" Alpine SWR-1042D Type-R subwoofer so the cone will be firing inward.
http://www.crutchfield.com/S-nxfHziX...0&I=500SWR1042'
Two reasons for this is that the total depth of the sub is about 7" which exceeds the tub depth of 4". Also, over the years of playing with car audio subs, I've tended to prefer the "dispersed" bass quality out the backside of the sub. It seems to have a smoother quality and it doesn't have a directional compression wave which tends to rattle things the cone is facing. The basket side will simply protrude about 4-5" through the stock square sub grate into the cargo area. This should affect cargo space minimally since it's off to the side and off the floor.
2) Second option is to do what reptile did. This would offer a completely stealth install with no compromises and a 12" cone surface area for possibly higher SPLs. My only hesitation is that SQL and bass extension will be compromised. Also, since it's hidden completely behind the stock siding, I am worried about possible rattles and vibration. I may want to cutout an opening for a real grill.
FYI, I will be powering the subs with 300W RMS.