I finally came across your thread and what an excellent job. From one anal retentive, gizmo and audio nut to another...AWESOME!
My biggest project to date was my 4Runner and when I started it, there were so few pics and guides to go by, so I created one myself. Since then, many people have benefited from the hard work and so they have/will from yours. Keep up the great work.
Any chance you did any photo doc of the sub finishing? I have only done about a dozen glassed enclosures in my audio projects and I always like seeing people's work! I have gotten somewhat lazy as my truck is "just a work truck" now, so very simple box designs and sprayed on finishes. With those subs, I assume you lost the 10"'s that the speakers are and then probably another 2"-3"'s for the MDF and surround surface as far as space in the back?
I installed 12's and only lost 6.5"'s, but did not have as much equipment to install as you. One other idea is to build a wall compartment in the front wall of the bed and seal some of the electronics in there. a surface mounted, glassed and sealed box with all the components you have slated for the inside back wall would neatly fit there and you would not loose as much space for narrowing a sub box...
I did an install like this for a buddy on a F150 with a hard cover a couple of years back and it worked perfectly. It allowed for all the electronics to be spaced out and easily worked with anytime he wanted. The entire enclosure was water tight as well as having the
tonneau cover over it for sealing out weather.
Hopefully some of this helps or stimulates the imagination....ENJOY!