The investigation into the assassination of U.S. District Court Judge John H. Wood Jr. unfolded in often painstaking steps, but its main focus changed little from the morning of May 29, 1979, when Wood was killed by a single rifle shot as he stood in his condominium parking lot in San Antonio.

For years, federal prosecutors in the Southwest had been at war with an El Paso family of Lebanese immigrants known as the Chagras. At the time of the slaying, Wood was scheduled to preside over the drug trial of Jamiel (Jimmy) Chagra, who the government believed was a major figure in the drug traffic along the border.

From the early days of their investigation, federal officials never wavered from their belief that Jimmy Chagra was at the heart of the murder.

More than a year ago, FBI Director William H. Webster announced that the government was "close to a solution" in the case. "We know the players," he said. "The question is the adequacy of proof."

Today, with indictments in and a trial to come, the issue of proof still hangs over the federal government. It is why the investigation into Wood's killing lasted nearly three years, cost almost $5 million and ended up as the most massive FBI probe since President Kennedy's murder.

On Thursday a federal grand jury in San Antonio indicted five persons in the Wood case. Charged with murder were Jimmy Chagra, now in prison on a drug conviction, and Charles V. Harrelson, a once-convicted hit man also in prison on separate drug charges. The indictment alleges that Chagra paid Harrelson $250,000 to murder Judge Wood.

Also indicted were Jimmy's younger brother, Joe; Jimmy's wife, Elizabeth, and Harrelson's wife, Jo Ann. They were charged with conspiracy to murder Wood and with obstruction of justice.

To nail down the indictments, federal officials took risks. They secretly taped conversations between the two Chagra brothers and between Joe Chagra and Harrelson. Joe Chagra claims that the information obtained is not admissible in court because he was acting as an attorney to both men.

In addition, officials taped conversations between Jimmy Chagra and another prison inmate who had agreed to cooperate with the government.

Joe Chagra fought for a year to avoid being indicted as a co-conspirator in the murder, and the battle over evidence is likely to be central to the upcoming trial.

But the three prosecutors expected to try the case--including a husband-and-wife team--have a reputation for underkill. "They're the kind you want to try a case like this," said one San Antonio lawyer. "They don't bite off more than they can chew."

Federal officials first tangled with the oldest of the Chagra brothers, Lee. He was a flamboyant defense lawyer who made a reputation--and a small fortune--by besting the government in a series of drug cases. "It will be just me against the United States of America," he said once. "I wouldn't want it any other way."

Lee Chagra was murdered in December, 1978, and a few months later Jimmy was arrested on drug smuggling charges. Jimmy, in the shadow of Lee's brilliance, had turned to the seamy world of drugs, sex and gambling. He was well-known around Las Vegas, and in one three-day gambling period lost $1.1 million.

The youngest brother, Joe, was the most quiet, a lawyer with his oldest brother. When Jimmy was arrested, he was suddenly the family spokesman. He also became embroiled in the Wood investigation.

Although Jimmy Chagra was a target from the beginning in the Wood slaying, the investigation moved slowly until, late in 1980, control was shifted from the U.S. attorney in San Antonio to the Justice Department in Washington.

In February, 1981, federal agents armed with search warrants went to Joe Chagra's home in El Paso and to the homes of four other family members. Methodically they moved through the houses gathering evidence, including tapes of conversations between Joe Chagra and Harrelson and a rough map that supposedly showed where Harrelson had left the murder weapon. They also collected drugs.

A month later, a new grand jury was sworn in, and it looked then as if indictments would quickly follow. But the map had produced no murder weapon and some of the evidence collected was of questionable value in a trial.

The prosecutors quietly continued their pursuit of additional evidence and spent months trying to pit the central characters in the case against one another, hoping one would agree to testify for the government.

Last summer, a major break occurred. A rifle stock was discovered near where the map located the murder weapon, and federal agents traced it to Jo Ann Harrelson.

She was tried and convicted of purchasing the weapon under a false name, and during the trial an FBI agent testified that the rifle had "the same . . . characteristics" as the one that killed Judge Wood.

Lawyers who have followed the case believe the government was successful in persuading one of the family members to testify against the others. She is Teresa Starr Jasper, Harrelson's stepdaughter, who was jailed last year on contempt charges for refusing to testify to the grand jury. She appeared before the grand jury this week and was not indicted in the case.

One reason the investigation took nearly three years is that the stakes are high. A comment made a year ago by Joe Chagra now rings with irony. "They do not want to blow this case," he said. "The worst thing that could happen is for them to indict someone and lose. So I think they're taking two steps back to take a close look."

Said a San Antonio lawyer, "It's one of those cases where you pack your toothbrush when you go because you better not come home if you lose it."