6x9's are a waste of time.
take them out, leave the hole open and install some sort of sub in the trunk.
If you're getting rid of everything then you'll need a new head unit, amp for the sub and new speakers for up front.
Get 6.5 component speakers and put the tweets in your stock tweeter location.
You'll also need an amp wiring kit for the sub amp. single run of 4 gauge should be fine.
Any halfway decent 12 in a sealed box should do quite well.
If you want a GOOD 12 I'd reccommend the TC Sounds LMS-R 12" from here:
TC Sounds LMS-R 12" DVC Subwoofer | Parts-Express.com
Or if you want to cheap out this one:
TC Sounds Epic 12" DVC Subwoofer | Parts-Express.com
Or this:
DIYCable.com : Intro » Home » Exodus Subwoofers »
The last one is a balance between the two.
Less bling but still should work well.