Christopher, I think you're being a little intentionally dense on this one. I wasn't concentrating on the metatextual part of the story, I was using the references that I caught to add depth to motivation, etc, within the story. That's why they're there, after all - to refer to earlier events that then inform the events we're seeing in the book.
But that's just it. I was responding specifically to your statement that "The problem was that the book had so many of those cute little references in it that it became hard to tell what was new and what was winking at past stories." But references to past stories and to newly invented backstory both serve the same in-story purpose to inform the events of the book and add depth to motivation etc. So if that's what you're concentrating on, then why do you consider it a problem that you can't tell the difference?
I love KRAD, and think Articles is one of the four or five best Trek books I've ever read. But in this particular case, I think the continuity references were often for their own sake rather than for the sake of the story. It made me feel as though I was missing something, even when I wasn't.
Ahh, I think this clarifies what you were saying. It's not that you couldn't tell which references were original and which were to past episodes, it was that you couldn't tell whether the references were plot-significant or merely continuity nods for their own sake. The problems wasn't confusion over the source of the refs, but confusion over their meaning. Is that about right?