MG88

I was told that rubberized undercoating works good to seal the box better. Not positive it helped anything but I thought it was worth a shot. I also added a wood dowel in a weak spot, it has a very slight interference fit and is glued in. Some use silver HVAC tape to smooth out airflow and seal things up better.

I think the rough design you made could be done and sound very similar to a "more square" box. I'd add something like recycled denim insulation to the back of the box(inside) to attenuate the backwave so it's not fighting itself if the mounting depth is tight. Just make sure the pole vent can breathe. My setup is something similar (shallow mount), it sounds better with some denim insulation behind the sub, it plays lower too.

Can you remove the box from the vehicle and play music to see if the sound goes away? Maybe there's a clearance issue with the box, or maybe the magnets are too close to the back.

You bet, make do with what you got. Ingenuity and creativity at work is half the fun. Drilling through a scrap piece of wood works too, using it as a pilot hole.

You could check http://www.bcae1.com/ It can explain thoroughly why. It's been a great resource for me in fine-tuning my system and giving me ideas on how to improve it.

Interesting, If they're going in their own dedicated box, I think the performance between one speaker and the next will be much more subtle. But I could be wrong, as I haven't experimented using cheap speakers vs high end speakers in the same box.

Just from my estimation using the photos, the first/top choice would sound better because the back of the speaker seems to be more isolated from the front, and more rigidly mounted. This should sound better overall from judging the photos. I might add some cotton insulation to the enclosure to reduce the echo.

As far as getting a warm sound or decent mid-bass, I find closing large access holes in the door skins helps a lot, the music is less muddy, better separation between the instruments. I got great results doing this just using some inexpensive Boss 6.5" speakers. They sound excellent now.