John Cofer studied law and eventually acted as criminal attorney for Clark, Thomas and Winters, a law firm headed by Edward A. Clark. Cofer represented Lyndon B. Johnson when he was accused of ballot-rigging when elected to the Senate in 1948.
On 22nd October, 1951, Mac Wallace murdered John Kinser. According to Barr McClellan, the killing had been organized by Edward Clark in an effort to prevent Kinser talking about a scandal that involved Lyndon Johnson's sister, Josefa. Cofer was appointed as Wallace's attorney. At his trial in February, 1952, Wallace was found guilty of murder. Eleven of the jurors were for the death penalty. The twelfth argued for life imprisonment. The judge overruled the jury and announced a sentence of five years imprisonment. He suspended the sentence and Wallace was freed.
Cofer also represented Billy Sol Estes when he was rumoured to be involved in a financial scandal that was linked to Lyndon B. Johnson. Estes ran a vast scam getting federal agricultural subsidies. According to Estes he obtained $21 million a year for "growing" and "storing" non-existent crops of cotton. On 3rd June, 1961, Henry Marshall, a Department of Agriculture official investigating Estes was found dead near Bryan, Texas. According to Barr McClellan, Marshall had been murdered by Mac Wallace. However, officially it was decided that Marshall had committed suicide.
On 4th April, 1962, George Krutilek, Estes's chief accountant, was found dead. Despite a severe bruise on Krutilek's head, the coroner decided that he had committed suicide. The next day, Estes, and three business associates, were indicted by a federal grand jury on 57 counts of fraud. Two of these men, Harold Orr and Coleman Wade, died before the case came to court. At the time it was said they committed suicide but later Estes was to claim that both men were murdered by Mac Wallace in order to protect the political career of Lyndon B. Johnson.
On 24th June, 1962, Senator John McClellan of Arkansas announced that his Permanent Investigations Committee would be looking into the activities of Estes. On 27th July one witness testified that Lyndon B. Johnson was getting a rake-off from the federal agricultural subsidies that Estes had been obtaining.
The trial of Billy Sol Estes began in October 1962. Cofer refused to put Estes on the witness stand. Estes was found guilty of fraud and sentenced to eight years in prison. Federal proceedings against Estes began in March 1963. He was eventually convicted of fraud regarding mortgages of more that $24 million. Estes was found guilty and sentenced to fifteen years for fraud and conspiracy.
In the excitement of the big trial, Estes tried to get rid of Cofer as his attorney. Cofer refused to be fired, saying he had already been paid. The next unpublicized issue between lawyer and client was whether Estes should testify or not. Estes was ready to talk, believing he could still charm anyone. Cofer was just as determined to keep Estes quiet, for the sole purpose of protecting Johnson. Estes might say too much and make things worse. On the other hand, Estes might convince the jury and get off. Like it was with Wallace in the Kinser case, there was no alternative, Estes had to be found guilty. Then anything he said later could be discredited. Estes grudgingly agreed. Cofer stayed with Estes.
A Texas Ranger, Clint Peoples, had befriended Estes and convinced him that he should come clean with the whole truth. True to his word, Estes agreed to appear before a Robertson County grand jury and clear the record concerning the cotton allotments, the death of Henry Marshall and the involvement of LBJ and others. He recounted the whole ugly picture - from the millions he had funnelled into Johnson's secret slush fund, to the illegal cotton allotment scheme, to the murder of Henry Marshall.
Estes testified that Lyndon Johnson, Cliff Carter (an aide of LBJ), Malcolm Wallace and himself met several times to discuss the issue of the "loose cannon" - Henry Marshall. Marshall had refused a LBJ-arranged promotion to Washington headquarters, and it was feared that he was about to talk. Johnson, according to Estes, finally said, "Get rid of him," and Malcolm "Mac" Wallace was given the assignment. According to testimony, Wallace followed Marshall to a remote area of his farm and beat him nearly unconscious. Then while trying to asphyxiate him with exhaust from Marshall's pickup truck, Wallace thought he heard someone approaching the scene, and hastily grabbed a rifle which customarily rested in the window rack of the truck. Quickly pumping five shots into Marshall's body, Wallace fled the scene.