Instead of 6X9's in back I would consider an array of 6's and a couple of tweeters - possibly some 3.5 or 4" - I don't like 6X9's. Shouldn't be too difficult to have a custom enclosure made to acommodate this.
In my 83ZXT I have a Sony CD head unit, CD changer, ADS speakers with the 5 1/4's in custom enclosures on the doors, the tweeters mounted in the door about 6" above that. A Hafler 100 w/ch amp feeds these.
I have a simple set of Pioneer 6.5" coaxes powered by a Rockford Fosgate Punch 22 in the stock behind the seat location for rear fill.
I have an Audio Control Eq/Crossover for the front and (yes I DO USE a) subwoofer - a Competition 12" in a 1.75 cu. ft. enclosure powered by a R-F Punch 100. The enclosure has the CD changer and Punch 100 attached to it so that I can remove the whole rig if I need to haul something.
This was all put together over 9 years ago. It's not the loudest but it is accurate, and I can hear it well with the t-tops off on the freeway at illegal speeds.
I did put DynaMat in the doors...