It's actually easier to make a good sub box with 3/4" MDF than with fiberglass (unless you happen to be a wiz with 'glass, in which case go for it). There's actually a surprising amount of space once you remove the storage cubby. Here's a short summary of the procedure - we can dig into details via PM if needed:

- remove the side panel to access the cubby (if I remember right, I needed to remove the rear trim first)
- take some cardboard and start mocking up some boxes. Start basic and push out into the edges of the space as you make successive boxes. Take your time - this is the most important phase.
- you should have the box extend below the floor of the trunk into the lower fender well. This will give you more volume, and you'll use the two mounting holes along the edge of the flat section of the floor that the cubby was mounted to to bolt the box in place.
- max sure the box comes near the top mount point for the cubby. I took a small piece of flat steel and cut it and twisted it to mount the top of the box. With the three mounting points, the installation is absolutely rock solid - no matter how hard I crank it, the box never moves at all.
- build the box out of MDF to match the mockup you've made. There's obviously alot of work in this step - having woodbworking tools is pretty well a necessity. If you don't have any (at least a tablesaw), find a friend who has them and borrow them or have them help you.
- mount the box to the three mounting points.
- use a sharp utility knife to cut off the cubby door (you can always reattach it with hinges if you ever want to restore the car to stock - this is the only actual change you will need to make to the car)
- trace around the inside of the cubby opening onto a piece of MDG and cut it out (you'll use this below)
- reinstall the side panel - you'll notice that because the cubby opening is recessed, the surface of the box is about one inch in from the outer surface of the panel. Place the piece you just cut above so that it fills the cubby opening. This will raise the surface of the box to better match the outer panel, and give you a double-thickness of MDF to mount the subwoofer to.
- using the template that came with the sub, mark where to cut the speaker hole. Remove the side panel and box, and cutout the hole for the speaker.
- reinstall the box and side panel.
- one more step to finish off the box - using the cubby door you cut off before, trace the outline of the door onto a piece of 1/4" pressboard (much denser than MDF). Cut out the hole for the speaker, then cover it with leather or imitation leather (or whatever you prefer) - this is the finished panel you see in the picture I posted above. I found imitation leather that match the color, feel, and grain of the interior leather at my local fabric shop. It will also nice fill the space left by the cubby door.
- drill your holes through the pressboard and two layers of MDF, then install the speaker

I used this Polk 10" dual voice coil sub. See previous post for details on hooking it up. Whatever sub you choose, as long as it has similar mounting depth and enclosure volume requirements you should be fine.