Without going back to the Yamaha drawings to check, it looks good to me. Did you find a source of magnets like that?
Looks pretty ravagey to me. Now we know it's a pleated diaphragm, so thanks for doing that. As for why HOK (and others) sometimes made drivers where the holes lined up perfectly and sometimes not, I don't know. Since you said you notice a change in the sound with a slight alignment, I was thinking hey, maybe they're doing it to tweak the FR of drivers so they match more closely, but that sounds too crazy to be true.
Oh, and it has occurred to me that if Royer can make powered ribbon mics and KRK and Prodipe can make powered speakers, why not powered headphones with motional feedback and dedicated EQ and the whole works?
Well er, um, size springs leapingly to mind. Not too sure I'd like to go back to the 70's with massive cans with knobs and geegaws sticking out all over:)
Allthough an amp the size of an e5 should be easy enough to integrate. Then again you have any add on's dictating the size and shape of your acoustics (think wireless headphones.....eek).
On the lined up magnet hole issue. I would be surprised if there was the level of hand made production involved which would allow for various alignment adjustments. I would think that would be cost prohibitive