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In 1983, Cristol was appointed an honorary professor of the Naval Justice School. During the 1980s, he was sent to the International Institute of Humanitarian Law at Sanremo to lecture on Law of Naval warfare.
After retiring in 1988, Cristol became a civil lawyer, and served as Special Assistant Attorney General of Florida. In 1985, he was appointed chief U.S. bankruptcy judge of the Southern District of Florida.
He also became an adjunct professor at the University of Miami School of Law, teaching Reorganization in Bankruptcy. He enrolled in the Graduate School of International Studies of that institution, where he spent ten years researching the USS Liberty incident of 8 June 1967. In 1997, he earned a Ph.D. degree on this work. In his Ph.D. thesis, Cristol analyzed the official investigations of the Liberty incident and conducted 458 interviews. Freedom of Information Act requests were used to obtain declassification of the Clark Clifford Report, 22 hot line messages, 22 National Security Agency documents and 31 National Security Council documents. Cristol was also able to obtain classified Israeli documents. The conclusion of the thesis confirmed the official investigations and demonstrated that the attack on the USS Liberty was a mistake.
Following completion of the thesis, Cristol sued the National Security Agency under the Freedom of Information Act and in 2004, the agency released audio tapes collected by an NSA unit aboard a Navy Lockheed EC-121 Warning Star aircraft flying near the scene of the USS Liberty attack. Subsequently, he published a book about the Liberty incident, "The Liberty Incident: The 1967 Attack on the U.S. Navy Spy Ship". Cristol said the tapes show the attack was an accident, and that the Israelis mistook the ship for an Egyptian one. However, on 2 October 2007, the Chicago Tribune published a special report into the attack, containing numerous previously unreported quotes from former military personnel with first-hand knowledge of the incident, which cast doubt on Cristol's conclusions.
In 1998, Pan Am sold to Guilford Transportation, in a transaction which removed Pan Am from bankruptcy. Consequently the company honored Cristol, who presided over the speedy reorganization, by naming one of their 727-225 aircraft, (Registration number N361PA), the Clipper A. Jay Cristol. After presiding over the reorganization of Arrow Air, he was honored by having an Arrow Air Douglas DC-8-62 (Reg. N8968U) named the "Judge A. Jay Cristol."
Cristol is a founding member of the National Museum of Naval Aviation at the Naval Air Station in Pensacola, Florida and a founding member and historian of the Wings Over Miami aircraft museum in Miami.
In 2003, the Greater Miami Aviation Association honored Cristol with their Glenn Curtiss Award which recognizes the contributions of an individual to improve the South Florida community. On February 1, 2007, St. Thomas University School of Law honored Cristol with its Outstanding Jurist Award.