I'm running a US AMPS 1000 watt digital amp.  It's the one on the bottom in the pictures.  The one on top is their 300T tube amps that puts out 150 watts per channel to my MB Quart mids and highs up front.
I checked the baffle out because the picture really makes it look off, and it was by almost 1/4".  I didn't notice it before.  
I beat the baffle down more and put some polyfill in it.  It plays deeper and the hollow upper bass sound is gone.  I decided that it was good enough and that I'd go ahead and seal it.  Just before I did that I thought what the heck and beat the baffle down some more, then I sealed it up.  I'm letting it dry now but I think I'm going to be happy with it now.  It was sounding decent so I'm going to live with it this way for a while.  
I think that the biggest problem was that I didn't think I could cover the port with the baffle without killing the sound.
Here's some of the latest pics.
http://www.computerwrestlers.com/Box_pix/Sub%20001.jpg
http://www.computerwrestlers.com/Box_pix/Sub%20007.jpg
http://www.computerwrestlers.com/Box_pix/Sub%20012.jpg
http://www.computerwrestlers.com/Box_pix/Sub%20013.jpg

Sorry about pics not working right.  The first two I forgot to put in a 0, but the last two worked.  They are all working now.  I guess I should have checked the links when I posted it.  I was in a hurry.
The sound now is good.  I'm happy with it.  I can't tune the crossover above 80hz or it starts to get that nasally sound again.  But now I'm feeling the bass and hearing it vibrate things like the CD cases that are in the door pockets.  Much better now, and I'm enjoying it.  Although I want more, so I'm still going to do my original idea and put some subs under the front seats.  It's just a bigger project than I have time for right now.  I only built the DB as an experiment to get more bass than I had .  Which now that it's tuned better is happening.  You were right about it playing lower but not as loud.  My biggest problem is that I haul a lot of stuff and really didn't want anything back there.  At least with this box I can stand it up when I need to and it doesn't take up as much room that way.  I would also like to build a box to put in it that really jams for those times when I want to get crazy!  Maybe a WO would be a good project and then I could store it in the living room when I'm not using it in the car.

Looks like your half moon port is not correct. When I look at your pictures it's not wide enough. This cranks up the tuning frequency...

erix has a good point-your half moon does look a little small? did you cut it to the exact measurement?

Good catch 60!

I try to keep my nose out of here since I don't have a DB, but stuffing in the motor is always bad news. CAREFULLY remove it and make sure you get it all. Another point ......... the port doesn't look the same as other pics I've seen. It definitely looks too small.

You guys are probably onto the root causes of the poor performance.  The port looks like it was cut with the centerpoint on the bottom rather than "x" dimension below.  

Mrchet check the 2.6" dimension and see if it is not 3.5" instead.  If this is wrong you should be able to set your baffle about 2.6" from the bottom and then use a Dremel or jigsaw to carefully "widen" the port.  This I think should help with the low end freq while moving the baffle back up to a more "normal" position should bring back the "punch" you are now missing.  

Now I tell you after you've already got the baffle sealed!

One other thing I did was use some weatherstripping for a gasget on the top.  Even with a very snug fit mine still leaked without a gasket.  Any leakage will cause cancellation and distortion.

Good Luck