Only 14 of those have been arrested and Mr Pearl's actual murderers are unlikely to ever face trail the investigation found.
After his kidnap, he was handed to an al-Qaeda gang led by Mohammed, a strategist for the terrorist network, who killed him.
The inquiry by academics, journalists and students involved hundreds of interviews with American and Pakistani officials.
Mohammed was captured in March 2003 and confessed to masterminding the 9/11 attacks.
The al-Qaeda number three is held in Guantánamo Bay military prison and has also previously confessed that he beheaded Mr Pearl.
However, doubts have surrounded the confession, because it may have been extracted under 'water boarding' torture.
The Pearl Project found Michael Dick, an FBI investigator, used video of Mr Pearl's beheading to create stills of the hand of his masked killer.
The photographs were shared with CIA colleagues holding Mohammed, who used a forensic technique called "vein matching" to determine the hands belonged to the same man.
They replied: "The photo you sent me and the hand of our friend inside the cage seem identical to me." Both the CIA and FBI use the mathematical modelling technique, though it is not considered as reliable as fingerprinting.
The investigation found Sheikh, who studied mathematics at the London School of Economics, orchestrated the kidnap and originally considered a ransom, but was later sidelined when Mohammed became involved.
The conspirators were "inept, plagued by bungling plans, a failure to cover their tracks, and an inability to operate cameras and computer equipment," it said.
An incompetent cameraman had failed to capture Mr Pearl's actual murder so the beheading was restaged moments later.
Sheikh was sentenced to death in July 2002 for murder and kidnapping and three others were given life terms. Their appeals have stalled.
Rai Basheer, a defence attorney, said the prosecution was delaying the process because it knew it would lose on appeal.
Raja Qureshi, a prosecutor, said: "I challenge the defence to come and attend the case properly and consistently, and they will themselves know whose case is weak." Federal officials decided in the summer of 2006 not to add Mr Pearl's murder to Mohammed's charges because they concluded that would complicate plans to prosecute him for the 9/11 attacks.