The 1999 report from the State Department that lists al-Fuqra as a terrorist group is "Patterns of Global Terrorism." Fuqra is listed on page 120.
The FBI document about the Muslims of America and al-Fuqra that Ryan Mauro references is available here: FBI Threat Task Force document. The document was originally secret, but was later made available in a redacted form. The assessments of the group highlighted in the episode are on page 15. The FBI lists the number of crimes involving MOA members on page 16, including 10 murders. The paragraph below is from the conclusion of the report.
The report on Jamaat al-Fuqra from the Regional Organized Crime Information Center (ROCIC) was funded by the Department of Justice. The assessment of Gilani as "an international terrorist" appears at the bottom of page 2.
The NYPD designated the entire al-Farooq mosque in Brooklyn as a terrorist organization for surveillance purposes in the years following 9/11.
Al-Fuqra has been linked to a series of terrorist acts in the 1980s and 1990s. The National White Collar Crime Center has also conducted extensive investigations into al-Fuqra in America. A map on page 21 of that report shows the locations of a number of those murders, firebombings and other crimes.
J. Millard Burr of the American Center for Democracy conducted an exhaustive investigation into the role of Sudan in Islamic terrorism. The report “The Terrorists’ Internationale: The Khartoum Venue” was released in 2013. The list of Islamist terrorist organizations identified by the U.S. prior to 9/11 (including al-Fuqra) appears on page 251. The chapter on the 1993 Khartoum meeting referenced during the episode starts on page 248, with the list of attendees (including Gilani and Osama Bin Laden) on pages 258 and 259. Gilani's attendance is covered in greater detail on page 269.
Sheikh Gilani's website references the Daniel Pearl case. In chapter seven, he writes "Obviously Daniel Pearl was to target me and then an assassination team would be sent in to kill me."
The quote on the commitment of Sheikh Gilani's followers came from a 2002 CBS News report.
The federal firearm case against members of the Muslims of America compound in Virginia is outlined in this Baltimore Sun article.
The Colorado case was covered extensively in the National White Collar Crime Center report. That document includes original photos of evidence from the trial, including explosives, weapons seized, the compound and the target labeled "FBI Anti Terrorist Team."
The press release from the Colorado Attorney General on the Tucson case: Attorney General on Sentencing of Khalifa Murderers
The full speech from the FBI Special Agent in Charge at a 2004 MOA event.
The exchange of emails with the FBI in which they declined to comment for this story can be seen here: FBI Requests We have redacted contact information for privacy reasons.
The document you see the mayor of Deposit, NY reading during the episode is from the FBI Threat Task Force.
This 2005 New York Times report mentions a Department of Homeland Security document that listed al-Fuqra as a possible future sponsor of an attack on America.