If you are not too picky, you can grab a cheap set of convertible rear panels that someone has aready butchered up with speaker holes and go to town on them. They come up for sale every now and then, some people give them away.
If you are really energetic you can use your factory panels for a fibreglass mold and create your own custom panel.
Same principle applies to door panels or kick panels.
As for a sub, pretty much anything will work in the trunk. You could throw the spare tire out and use it's hold-down to keep the sub in place.
A suggestion for the head unit to keep it stock appearing, contact a positive contributor to this board and all around good guy, "BigMoneyLewis" on here to set you up with something:
Link to his site.........