actually, i just looked at it, and if you were to make a box with outside dimensions 41.5 x 24 x 8, it would still fit with room for your targa top (im not sure abotu the interior panels though, becuase mine arent in the car right now ) the airspace would be about 4 cubic feet.
easiest thing to do is make a rectangular box, as wide as you can fit, and as long as you can fit, then figure out how deep it will need to be to equal the proper amoutn fo airspace you need.
if you need 2 cubic feet (about that for 2 sealed 10s) you can make the box 24 x 12 x 12 = 3456 = 2 cubic ft (inside dimensions). now as long as the answer still is 3456, you can change the numbers around. say that you need the box 6 inches deep for your subs to fit. so you could make is 48 x 12 x 6. but that is too wide, so you make it 28.8 x 20 x 6.
that would be 6 inches tall, 28.8 inches wide, and 20 inches long. that would fit nicely into your hatch, and not take up too much space. dont forget that is inside dimensions, so it would be 30.3" x 21.5" x 7.5" using 3/4" wood (MDF = medium density fiberboard is the best to use for sub boxes. easy to work with, very dense, and not too expensive).
most local lumber yards will even cut the wood for you too size for a small fee, so you can just take it home, glue and screw it together, and your ready to go.
dont forget, if you build a obx liek i described, you must brace it or else the box will flex, and you lose output.
I have a box that I built for my 87. I'll try to get pics as soon as I can. It held two 12's and fit under the targa. It took up the whole floor and went from side to side so it never moved. It also couldn't be taken out without taking out the targa attachment points. The only bad thing was no spare tire, which didn't really matter to me. There was still some room for cargo in front of the subs ontop of the amps (which were under plexi-glass)
The basic layout was (after removing the brace that the false floor hinges to) a sheet of MDF cut to fit the whole floor at the bottom. The box was built toward the rear (about 8-10" tall) and the amps were mounted on the front portion on top of the MDF. I built another piece of about 3/8" plywood and 1/4" board and put together a hinged floor above the amps (hinged to the box and went from the box to the back of the seats) The amps were two RF amp (360.2 and a 240.4) that were linked together. No wires and no bolts/screws showing. It ws also covered with vinyl that matched the interior. It almost looked as if it came there.
Still waiting for a buddy to scan a picture of it for me.