It seems to me that one of the biggest limitations is the selection of the sub woofer itself. Appearantly there is very close to enough space to mak a 12" diameter woofer fit, but the depth of the woofer seems to be the primary limitation.
I have been kicking around the idea of making an enclosure very much like the one in this picture:
https://docs.google.com/open?id=0B-S6rUG7e2O0MUMxQ2tCQ09LTms
but instead of mounting the woofer directly to the surface like this one, make a ring that is about 5/8"-3/4" thick. The ID of the rings would be just big enough to clear the area that the woofer requires to mount in. The OD of the ring would be a bit larger than the woofer. Maybe even as large as my cover plate (described below) will allow.
Now take that ring and glue it to a cover plate. This cover plate would be large enough to cover the factory cutout. It would be shaped to fit the contour of the wheelwell. It would run all the way to the back piller. From the floor to the top edge of the wheel well.
The cover plate/ring assembly would bolt on to the enclosure sandwiching the wheel well plastic in between them. Obviously some of the wheelwell plastic wil need to be trimmed to clear the OD of the ring, but all of that will be covered by the cover plate. The Woofer would then mount on to the cover plate. This will now give the woofer depth anothe 1 1/8" - 1 1/2" of depth. This design will also slightly increase the cabinet volume.
The final product would not officially be a stealth box because it will stick out of the stock location a little bit, but it will keep the sub enclosure in the stock area while increasing the sub enclosure volume and give you a nick cover plate to finish the area up with.
I am going to build this box......... someday! I will be populating it with a 10" sub though. I like the punch of a 10" better than the flutter of the 12" I have right now.
This will be my first sub box I have ever built, so hopefully I don't have too much to learn.