I agree with TrebleRebel that conspiracy theory has its limits. What I want to do is to see whether position 2 necessarily falls outside the bounds of plausibility. If it does, then I will have to revert to position 1, or some other theory entirely.
First, let's ask ourselves how many people would have to be in on the plot, if 9/11 and the anthrax letters were a joint effort between Iraq and al Qaeda. On the Iraqi side, there would be anthrax technicians, their handlers in intelligence, and their political bosses. On al Qaeda's side, there would be the 9/11 team, leaders like bin Laden, and their intermediaries with Iraq. Just as a concrete scenario, let's suppose that an Iraqi intelligence officer and a biotechnician went to Kandahar with Ames-strain anthrax, showed Yazid Sufaat and the future mailer how to culture and prepare it, and then went home; and then a few kilos of the stuff was transported to the USA by someone on the 9/11 team, who gave it to the mailer.
Not that many people are required! The Iraqi government and the al Qaeda network are (were) both large organizations, but it might require only half a dozen people on either side to put this together. Word would spread, and after the attacks their colleagues might suspect, but they wouldn't necessarily know.
On the American side, suspicions that the anthrax came from Iraq were there from the beginning, but they were just suspicions. The first chance to get hold of actual evidence would have come after the fall of the Taliban. So far as I know, the only public evidence of biological or even chemical weapons development in Afghanistan is the tape of a dog being gassed, found I think by Keith Idema. Supposedly there was a CBW training camp in Herat in 2000, run by Zarqawi, and (as piasa posted above) supposedly Yazid Sufaat ran an anthrax program in Kandahar, but so far this is just hearsay - I don't think either of these claims features in any official, on-the-record statement.
It seems that al Qaeda's leadership dispersed into Iran and Pakistan, and that they did destroy some of their records before leaving. So, continuing our scenario, the evidence left in Afghanistan might have been grabbed up by Special Forces and shipped back to the USA for forensic analysis by CIA WMD specialists, only to be found circumstantial and equivocal. However, the picture would have to change as al Qaeda's operatives were chased down around the globe, and especially once Iraq was occupied and the Ace of Spades tracked down.
Let's ask who, among the US forces that entered Iraq, would be in charge of looking for evidence of an Iraqi connection to 9/11 and the anthrax letters. The immediate job was to defeat the Iraqi army and occupy the country. Locating and neutralizing battlefield WMDs was certainly part of the planning, but that's not what this scenario is about. As we all know, the regime just melted away - they went underground in order to organize a guerrilla war. There was a Baathist directive to destroy records in the event that the invasion was successful - I imagine that this was part of the looting and general destruction which followed April 9th. Once the country was occupied, the Pentagon's Office of Reconstruction took over the civil government, and the intelligence people could start trying to figure out what had happened to Saddam. That is the first point at which the search for evidence of a link to 9/11 could begin. One would look for a paper trail, for physical evidence of anthrax labs or training camps, for scientists and intelligence officers who played a part or who heard about the scheme, and ultimately one would start to capture the former Iraqi leadership, interrogate them, and combine that with the intelligence coming from the global war against al Qaeda. That's the context in which to judge the plausibility of position 2 (or even of position 1). I hope to get a handle on this in a future post...
US fights war with Iraq. Troops are supposed to leave Saudi Arabia once Saddam Hussein is defanged, but they stay on while UN weapons inspectors and Iraqi intelligence have an endless fencing match over a hidden WMD program. Concurrently, an unprecedentedly ambitious form of terrorism begins to strike at the USA. An undeniable attack in 1998 leads to a pro-forma response against the terrorists, and then the adoption of regime change as official policy towards Iraq for the first time. The WMD inspectors are withdrawn entirely. There are rumors of WMD cooperation between Iraq and the terrorists. A new president comes to office, who intends to make regime change in Iraq the centerpiece of his Middle East policy. The terrorists plot their biggest attack ever, they pull it off, and a WMD shows up in the aftermath. Immediately there is a small war in Afghanistan against the terrorists, followed by 18 months of material and rhetorical preparation for war against Iraq. The chief terrorist (KSM) is captured, and then the war goes ahead.
All that is missing, to round out this picture, is vindication of the war in Iraq, in the form of proof that Iraq was behind the terrorism and the WMD threat. Apparently it's been so long that most people have given up on that idea. But, as my previous post indicated, it was never going to be easy to prove; and since no-one in either administration ever publicly blamed Iraq for al Qaeda terrorism, there must be a strong temptation to leave the past alone, especially now that Saddam himself is safely in captivity, and focus on postwar crisis management...