It's basically a matter of playing with the numbers until you find what works. I'm going to assume a 16 ft^3 box tuned to 32Hz for this example, with the subs and port both firing up.
Let's decide on a height and width, I'm going to assume 48" wide, by 24" tall based on your measurements, those will remain constant throughout our calculations. Don't forget that those are external dimensions, not internal. Assuming you use 3/4" MDF, internally, it's 46.5" wide by 22.5" tall.
Let's assume that there's 0.5 ft^3 of sub (like there is), and allow 0.2 ft^3 of bracing (round numbers for ease of calculations). Let's assume the port will be an L-port, running the width of the box, so 46.5" wide (internal dimensions), and let's make the port 5" wide, giving you 232.5 in^2 of port area.
For a 16 ft^3 box, to get a tuning frequency of 32.5Hz (I made a design change mid calculation so the tuning changed from 32Hz to 32.5Hz), with that port area, you need a 24.5" long port (taken from 12v's site). (46.5" x 5" x 24.5")/(12 x 12 x 12) gives us a port volume of 3.3 ft^3. Add that to the 0.7 ft^3 we allowed for sub displacement and bracing volume, and that gives us 4 ft^3 of volume that we must account for.
4 ft^3 of sub/bracing/port + 16 ft^3 of box = 20 ft^3 of airspace that must be factored into the box. Let's solve for the length of the box: 20 ft^3 = (22.5" x 46.5" x "X")/(12 x 12 x 12). "X" = 33" long (internally), so 34.5" externally + 0.75" for the thickness of the port wall on the inside = 35.25" long. Add 1.5" to the internal dimensions, and you get a box that's 48" wide, 24" tall, and 35.25" long.
So you external dimensions are 48" wide by 24" tall and 35.25" long, with a port that's 46.5" by 5", and 24.5" long. I haven't double checked the math or anything, but that gives you an idea of where to go with the design. You can go and double check the math if you want and use that design.
WARNING: I haven't double checked any math, or checked measurements with anything other than 12v's site, so don't use that design without going over the math and making sure it's all correct. I'm not responsible if that design isn't right. I'm not a box designer by trade, just a hobbyist. It takes a lot of time to do it right, and this was a quick design I generated, not a complete design that I've modelled up in sketchup and double checked like I usually do.