infinity reference subs and MTX boxes

I'd go with the MDF. Particle board isn't the best stuff to use for sub boxes, especially if it gets wet. How much are you spending for the subs? I'd personally go with the Kappas. If you're going with a sealed box, they are really easy to do yourself. For materials, it's only like $30, if that. You can be sure it's sealed properly and built to the right volume. Most pre-fab boxes aren't braced, also, so that is one thing that will add rigidity to your box.

You might notice a little increase in bass if you reverse the phase of one sub. It really depends on the car, though. You also might get a tremendous amount of cancellation. Just experiment. It only takes a minute to switch a couple of wires, and it shouldn't take long at all to notice a difference.