sell the 6x9s and your front speakers, then use the money for a decent set of front components, i would recommend focal or rainbow. Don't bother with speakers in the back, cos you don't go to a music concert and face the back do you, your brain prefers to have the sound coming from the front

Don't bother with mdf all over the place in the boot, it will only slow you down, and it is more to rattle about. Just a simple, tidy box, with maybe a bit of velcro to hold the sub to the boot floor if you need it.

My 12" JL sits in my boot, with the amp velcro'd beside it, and with all the wires hidden (nothing worse than having wires flapping about in the breeze all over the place). Simplicity is the key