re se12 enclosure

Because of the use of a corner brace inside the port, if you were to look at the port result as a straight line it would look something like this:

I'm not sure if I could explain what that type of constriction in the port diameter would do to the port function, but that kind of design should be avoided.  While you now have everything glued into place, it doesn't look like there's a fix that you could do for it.  The use of the corner brace is very good, but the opposing corner should have been cut so that it follows the same angled turn.

I agree with the above post on the subject of bracing.  You should incorporate a solid baffle with cutout type of brace in the center of the box.  It is a solid piece of MDF that is sized to exactly fit front-to-back and top-to-bottom, a large center hole cut out, and glued into place.  It looks like this type:

In looking at the pic, I don't see the results of excess glue removal at the seams nor along the seam of the double baffled face panel.  It appears like glue might have been used sparingly.  We should be able to see the glue excess pushed out along the seams (or the result of sanding / scraping off the excess).  If the front panels are not securely bonded to each other with glue, make sure you pull them tight to each other with screws before you cap off the project.  You could also add another corner brace to the far back corner.

Use plenty of glue before you put the lid on it.  If you see excess glue pushed out along the entire lengths of outside seams when you clamp it you can be satisfied that the top will not need additional caulking on the inside seams.  The center cutout brace can be glued and installed at the same time you install the top.  Before that, caulk every seam you have access to now.

Be sure to paint the inside of the visible part of the port before you cap off the box.  All in all, it looks like you are doing a very good job with it.

I disagree.

From a sonic perspective, I suppose this is not incorrect, however, taking into account the entire vehicular situation, I think this is poor installation design.  Unless the install is of the most *extreme* variety, bracing a box made of 3/4 MDF isn't going ever going to produce any sonically detectable differences.

3/4 MDF weights ALOT - and this thing is supposed to go into a CAR - it has to move around and be filled with >$3.50/gallon fuel.  Adding MORE weight on top of what is already a 3/4 MDF box is WAY past the point of dimishing returns - especially for any type of install that actually goes into a vehicle. At this point you are just slowing down ur car and using ever more unleaded - in these times, I think these are critical considerations!

Indeed - I actually think 3/4 MDF tends to be a waste of resources, but without getting into all that - I always build 1/2 MDF boxes with a coat or three of fiberglass resin on the inside - saving some ~40-50% mass and considerable external dimensions over a traditional 3/4 MDF box of identical volume.

If one absolutely insisted on bracing a box however - 

I do agree that this is, certainly, the best possible way to do it - the arch is an insanly strong shape. 

http://en.wikipedia.org/wiki/Arch

The realities of vehicles being what they are however,

Sadly, no box I've EVER designed to actually fit inside a trunk has "enough" volume.

What...did you say 120 volts AC?  How 'bout using a 12 V DC switch?

With that baffle misalignment, if it were me:  carpet will not hide the defect, but in fact will call even more attention to it.  Is the back panel jutting out 1/16" at all four sides?  Use strips of stock MDF and glue around the perimeter (make the 3/4" stock strips thick enough to be able to measure and cut...for example 3/4" X 3/4"). The strips will extend out past the misaligned back panel.  Carpet the back inset separately.  The rest of the box carpet would wrap around the new back edges and terminate at the carpeted inset.  Or it may be easier to carpet it in reverse of how I explained it, with the back panel inset being last.  Say that's how you designed it...it would be believable.