This is very frustrating. If Franz Joseph saw Jein's "Doe" article before drafting his blueprints, he could have used Jein's NCC numbers and the whole ST universe would have been in agreement.
But Jein's article is dated April 1975 (as reprinted at TrekPlace.com), and the blueprints were made in 1973.
Edit: Jein's article actually refers to the Booklet of General Plans. Was the first edition missing FJ's NCC numbers, or was Jein just ignoring them?
Is there no "MK IX" reference in The Making of Star Trek
, maybe in the chapter on the Enterprise? I'm at work now and can't check. That would be FJ's source then.