Hey man Ill add my .02 since Ive done this before and think I may as well put what I know out there and see if any of its of use to ya
Anyway, I think its cool that you are trying to be creative and use some tech tools but in all reality for a project like this, nothing is going to be better than a simple tape measure, a marker and some cardboard type paper (thick stuff)
What Id do is, go out to your jeep, takes some measurements with seats up and down, then get the exact sub/amp dimension for the setup you want. Then decided if you want to go ported or sealed box because the the port sizing for the tuning you want will need to be factored into total design as well as amp/sub placement in the box of course and how you want to seal each chamber off (if running two subs). Also think about covering the amp possibly for cargo/damage reasons but Id probably just let is sit flush and exposed, not big issue really.
Once you know those numbers, you can mach up the actual curves of the rear cargo area onto some cardboard paper directly in the back so your cuts will be spot on. Combine those with your length/depth measurements and trace it out onto your big piece of MDF. You should be cutting 4 pieces (face/back, top/bottom) total with open sides since their sealed by interior panels in that setup which is a very nice feature. The amp here is probably mounted to another small wood box inside this so thats something youll want to look into. Id get creative and mount on inside another so that comes up fliush to the outside face, just me though.
After its all cut, lay it out in the back before its assembled to check fit and make necessary cuts if any. (remember, you can always go smaller, real hard to add back on like cutting anything haha) Once its fit snug in the back, take it back apart and make your sub/amp cuts and also the rear plug hole cuts. Once you have all opening finished where you want, just screw it all together nicely (maybe some glue beforehand too pending how hard those things pump) Then just carpet it up and make the cuts on the carpet for the finished product! Pop your sub/amps in and secure with screws.
Also a tip, you may want to secure it down with those open-eye hanger type hooks that screw into wood (they latch over rear cargo tie downs on back seat) and they will hold that box nice and tight in back so you can drive without worrying about it sliding around haha
Ive done done boxes similar to this many times and this method has worked flawlessly for me. Just need to make sure you measure properly (to the t) and have a steady hand
GL w/ the project keep us posted, looks like a real clean setup!
FWIW, you could easily reproduce these things for wk jeeps too and make some $ I bet - Maybe some competition for the JL stealthbox which is priced way too high for what it is if you ask me