When they built the original mockup they weren't doing it from a computer model (I'd love to see the actual construction drawings). Indeed knowing that leads me to suspect that Phil Broad's drawings---and subsequently my own---are slightly incorrect.
I've pretty much reasoned out what I have to. It'll just be a bit tedious. The thing is my drawings "correct" certain things that look to be production compromises to facilitate construction. That adds a small wrinkle to the some of the shapes in the design. In like manner the saucer on the 11ft. filming miniature of the TOS E
isn't a perfect circle, but it wasn't noticeable on TV. Yet an actual scale replica of the ship demands a perfect circle for the saucer.
My shuttlecraft is, of course, an idealized version since there were significant discrepancies between the full-size exterior mockup, the interior set and the small miniature. For me this is what the "real" shuttlecraft is rather than a replica of a plywood set piece. Cary did much the same when developing his take on the TOS E.
Small adjustments are made for it to work, changes that will likely pass unnoticed unless pointed out.
A clue to the shuttlecraft's overall shape can be seen in those few photos showing it under construction where you can see the exposed frame members before the exterior walls were put on.