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Definitely lose the giant box. You can get excellent individual boxes for each sub to go in each corner of the hatch from a member here, although they do not come cheap. As you can see from my 8's, you should have enough room to do your 12's. 
I had a local shop fabricate these for me, that way the t-tops can still go in the back. Although it is a shame you had to go with an auto, it is still a Z and looks great nonetheless. Enjoy it.

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