The S1 was in production for some time. When the S2 came out it was changed to allow the car to pass US regulations. This meant the fuel tank needed to be moved more upright between the rear wheels.
This gave more boot space but reduced the rear shelf I believe. I will get a couple of pictures at the weekend and photobucket them for you.
The Focals I fitted really do have some guts. I can hear them clearly at 80ish with the lid down. Allegedly.
As for the 6x9 speakers. These do give a lot more punch but also need more depth, space and also stiffening as they really can move about when driven hard. If you are willing to pay a bit then some of the 2 part (bass/mid & tweeter) combinations around can give a surprisingly good effect for a lot less damage. Re the back panel protection in the footwell. Consider applying a Dave patch (neoprene)and metal deflector panel outside of it ?