Trying to figure this all out (aftermarket stereo system)

I'm sorry, I don't get that whole audio thing. You have a fastback with the drop down pass-thru door, and you are wasting all that space and convenience by blocking the door with all that junk.
That sub woofer looks dangerous if you were in an accident, maybe even a panic stop situation. Years ago, a Seattle Seahawk player was paralyzed by a subwoofer flying forward in an accident, and breaking his neck.
Why don't you mount the guts on either side of the dropped down door, or maybe in the spare tire well, so as not to negate the pass thru feature.