Ideally, I would do the dual 3" ports, however, they are fairly long. The single 4" port saves 3.5" on port length, but does not have as much port area.
Unless you are doing flexible tubing or putting a right angle bend on the port(s) one of the dimensions will be fairly large to accomodate the port. Square/rectangular vents are an option as well. They are a bit more work, but actually strengthen the enclosure.
Using a single 4" aero port I get external enclosure dimensions of 15" x 18" x 25.5". Or you could hang the port out side the enclosure and change the dimensions
Using dual 3" ports would require a larger enclosure. I would probably recommend doing a rectangular vent if you were thinking of having port area equal to dual 3" ports (14.14 sq. inches.)
These measurements assume the use of 3/4" MDF. The dimensions also allow for all of the displacement of the port, driver, amplifier and bracing.
I would recommend the port and driver on one of the 15" x18" panels. I do not have access to fancy animation to draw a design out for you though.
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