You're right, the AMI cases are the bridge between the hijackers and the anthrax letters. And if 9/11 and the anthrax were part of the same conspiracy, I'm not sure why the terrorists would see a need to deliberately create such a bridge. You would think that the content and the timing of the letters would be enough; they would hardly anticipate that the letters would come to be viewed as the work of an opportunistic domestic terrorist, who was just pretending to be a Muslim radical.
We are hindered in our deconstruction of the plot by the uncertainty which still surrounds the AMI cases. We don't know if the AMI letter(s) were part of the main media mail-out, or if they were earlier; we don't know if the J-Lo letter carried the anthrax; we don't know what it said; we don't know if there was a Star of David. We know next to nothing about the relationship between Mohammed Atta, his landlady, and her husband the AMI editor and amateur pilot - when and how they met, what sort of social contact they had.
However, here is a scenario. As The Hatfill Project regularly points out, the media mailings were postmarked September 18, the day on which the Atta-in-Prague story (and thus the connection to Iraq) was first publicly aired. I think there is also ample evidence that Iraq was behind previous Al Qaeda attacks, and that the US government knew it, but chose not to talk about it in public. Here, then, is the scenario:
The anthrax letter to AMI did indeed precede the main wave of media letters, and it was originally intended to stand alone. The puzzling, isolated outbreak of inhalational anthrax would have been part of the 'secret dialogue' between Iraq and the USA, a warning that going after Saddam would invite biological terrorism. However, officials started floating the idea of Iraqi involvement before the message got through, and so the keeper of the anthrax upped the ante, first mailing all the major media outlets, and then going after the politicians themselves when the war in Afghanistan began.
I find this scenario more plausible if the anthrax mailer is thought of as an Iraqi agent rather than as an Al Qaeda member. I imagine him as based in New Jersey, but travelling to Florida in order to meet with the hijackers and help them prepare the J-Lo letter.
I don't know if I quite believe my own theory here, but there it is, another scenario. One thing it suggests is that similarly subtle forms of blackmail - demonstrations of the capacity for bioterrorism - may have accompanied previous attacks, in ways that would only be noticed by investigators who knew what to look for. I think there was an article or two recently about anomalous anthrax cases early in the 1990s; one might want to see if they occurred in conjunction with previous Al Qaeda operations.