I think Isikoff gets one thing wrong. He writes:

In a federal terrorism indictment unsealed last month, Fitzgerald's prosecutors charged Major Iqbal — identified as Mazhar Iqbal — as a co-conspirator in the Mumbai terror attacks, alleging that he provided Headley with $25,000 to pay for his scouting trips to Mumbai and reviewed his selection of targets for the attack along with an LET operative named Sajid Mir.

Major Iqbal is not identified as Mazhar Iqbal. They are two different people. In the Second Superseding Indictment, defendant No. 5, Mazhar Iqbal, an alias for Abu al Qama, is an LeT operative. Defendant No. 6, Major Iqbal is another defendant, indicted as "FNU aka Major Iqbal." Although the Indictment doesn't refer to him as a Pakistani ISI officer, Headley's interviews clearly state he was.

The four LeT members and associates named in the Second Superseding Indictment are: Sajid Mir, aka Sajid Majeed, Abu Qahafa, Abu al Qama (Mazhar Iqbal) and someone referred to as "Lashkar member ‘D’. Major Iqbal is stated to be someone in Pakistan who provided Headley with the money ($25,000) to open the Mumbai office of First World, Rana's immigration business, and living expenses while he scouted out locations that later turned out to be targets of the Mumbai attacks.

Headley has said his ISI handlers were Major Iqbal and Sameer Ali.

Also unresolved: What agency Headley was working for when the U.S. sent him to Pakistan in December 2001. Was it still the DEA? Or a joint DEA-FBI terrorism task force? Or the CIA? December, 2001 is the same month the United States designated the Pakistani group Lashkar-e-Taiba as a terrorist organization. Less than two months later — in February 2002 — Mr. Headley began training with LeT. Headley said in interviews with Indian agents he decided to join LeT for jihad in 2001. Headley's interview is available here and here.

It was in 2001 that I decided to join the LeT and fight for the cause of jihad. Since my video business was not doing well, I rented it out and moved to Pakistan where my thoughts on jihad and Salafi Islam got strength.

On his training, Headley said:

It was in 2001 that I decided to join the LeT and fight for the cause of jihad...My training began in February 2002 when I went for the Daura-e-Sufa training of three weeks in Muridke. ...In August (2002)I went in for LeT’s Daura-e-Aam in Muzaffarabad. ... In April 2003 I underwent the three month long Daura-e-Khas at Muzaffarabad ...I was taught unarmed, close quarter combat in September 2003 where I came across an officer from the Pakistan Army who was an expert at this form of fighting and imparted training.

It seems, unbeknownst to the U.S., Headley had already turned before they sent him to Pakistan. Who might know? Probably DEA Agent Derek Maltz, now head of DEA's special operations, who recruited Headley in 1988 during his first heroin bust and reportedly was involved in his later cooperations. When did the U.S. figure out its worm Headley had turned? No one knows for sure. It was Britain that told the U.S. in 2009 that they thought Headley was involved in the planned attack in Denmark, which led to his arrest. The U.S. was reportedly clueless about his role in the Mumbai attacks until he told them, after his arrest.

Who is the unnamed "Lakshar Member D" in the Indictment? From this leaked Wikileaks cable dated April 30, 2009, it may be Saifullah Muzzamil (aka Muzzamil Bhat), leader of an LeT sub-group working under the direction of LeT operation commander Zaki ur-Rehman Lakhvi. (Another of Muzzamil's aka may be Yusuf Abu Gurera.) More on that here.

On Headley's ISI handlers, he said:

My ISI handlers in Pakistan were Major Sameer Ali and Major Iqbal. With Sameer, I was generally in-touch over phone and email. Iqbal was I think in his mid-thirties and introduced me to the higher-ups in ISI. One of them was his boss Lt Colonel Hamza. I was the one who apprised them of our complete plan to attack India in my first meeting with both the men. The Lt. Col assured me of all help and said I must follow instructions from Major Iqbal. The latter provided me with USD 25000 for my India trip. They also gave me counterfeit Indian rupees for use in Pune.

Major Iqbal is a very professional man. He assigned a non-commissioned officer of his to train me on the basics of intelligence like how to create sources, how to take cover and so on. I was asked to apply these techniques on the streets of Lahore and I really enjoyed it. This was a much more scientific and effective training as compared to the LeT modules.

According to Headley, LeT and Pakistan's ISI were jointly responsible for the Mumbai attacks.

I think the LeT and ISI plotted the Mumbai attacks to shift the interest of the world from Afghanistan and to instill a new spirit among their own cadre which were getting restless to join jihad in that country.

...[The]Mumbai attacks were financed and supported by the ISI, pretty much like every other plan of the LeT is. Every important LeT member is handled by ISI officials. My handlers were Major Iqbal and Major Sameer Ali. Similarly Lakhvi was controlled by Brigadier Riyaz who is based in Muzaffarabad. Major Iqbal provided money for my surveillance in Mumbai....

As to his ISI handlers:

I was the one who apprised the ISI officers of our complete plan to attack India in my first meeting Major Iqbal and his boss Lt Col Hamza.

...At the meeting, Major Iqbal and his boss, Lt-Col Hamza listened to my plan for two hours. Assuring me financial help, Lt-Col Hamza directed me to follow what Major Iqbal says and inform him of my activities.

Headley told the Indian interrogators that he stayed in touch with LeT's Abu Qama, aka Mazhar Iqbal, when he surveyed likely targets in Mumbai. After the Mumbai attack, Abu Qama told Headley that he didn't want the ISI's involvement revealed.

Also after the Mumbai attacks, Major Iqbal advised Headley not to contact anyone until further notice and to remove any incriminating materials from his home in Pakistan.

If it's hard to keep straight the Pakistani military officers from the ISI officers, it's probably because in Pakistan, Army officers are promoted to the ISI and then listed as having retired from the Army. One probable example: Maj. (retd.) Abdul Rehman Saeed, named in the Rana Indictment as having worked with Headley, using the aka Pasha. Pasha worked for both LeT and Ilyas Kashmiri's Brigade 313. Another ex-army officer who worked with Headley is Major Haroon Ashique, who worked with Ilyas Kashmiri. According to Headley, Ilyas Kashmiri had become al Qaeda's number 3 leader in Pakistan.

The Government wants to focus solely on LeT at Rana's trial. Clearly, it does not want to reveal or have to bring any action against the ISI for its role in the Mumbai attacks. Rana, of course, wants to bring up the role of the ISI.

Also, Rana has said in court pleadings that the Mumbai and Denmark plots involved separate organizations. Rana says LeT withdrew from the Denmark plot in March, 2009, and it was taken over by Ilyas Kashmiri. The Government argues that LeT was involved with both. The Court, at least on the joinder issue, sided with the Government.

Headley says every LeT member had a Pakistan ISI official as a handler. His were Major Iqbal and Sameer Ali. India hopes Rana's trial will reveal their true identities. It will be very interesting to see how much the Court restricts Rana's cross-examination of Headley, which could reveal the answers.