Lynn, who as secretary of clergy from 1992 to 2004 ran the office that recommended priests' assignments, is the first church official nationwide to be tried for allegedly enabling or covering up clergy sex-abuse.
His codefendant, the Rev. James J. Brennan, is charged with attempting to rape a 14-year-old boy in 1996.
Both have denied the accusations.
Wednesday's testimony created an uncomfortable but potentially recurring scenario at the trial: a parade of priests taking the witness stand and discussing the sexual habits or proclivities of other priests, all for the prosecution of a monsignor that all knew and some clearly liked.
Much of the testimony was devoted to Murtha.
In 1995, the Rev. Joseph F. Okonski testified, he found S&M magazines and videos in Murtha's room when both priests were assigned to St. Anselm parish in Northeast Philadelphia.
Under questioning from Assistant District Attorney Jacqueline Coelho, Okonski said he began regularly checking Murtha's room. He later discovered the letter Murtha wrote in childish handwriting to a seventh-grade boy at the parish school.
According to Okonski, he reported the letter to the Rev. James Shields, the pastor of St. Anselm's, but Shields "did nothing."
Prosecutors have said they have no proof Murtha sent the letter or abused the boy.
Months later, archdiocesan officials became aware of the materials and confronted Murtha. He admitted they were his and was sent to St. John Vianney, a church-owned hospital, for evaluation and treatment.
After his discharge, Murtha was assigned to St. Ann Church in Phoenixville. The pastor, the Rev. John J. Newns, testified that Murtha acknowledged what had happened at his previous assignment, and that he was being monitored by a counselor and aftercare team.
That monitoring appeared to have ended by the time he arrived in Havertown.
McKee said Lynn told him almost nothing about Murtha's background when the secretary of clergy asked if he would accept the priest at Sacred Heart in 2002. Among other duties, McKee asked Murtha to train and manage the parish's altar boys and girls.
Under cross-examination by one of Lynn's lawyers, Jeffrey Lindy, McKee acknowledged that he never saw Murtha engage in inappropriate conduct with young men or children.
Another priest, the Rev. Michael Hennelly, said he learned about Murtha in 2005, around the same time McKee petitioned the archdiocese to transfer him out, citing Murtha's issues with "anger and authority."
At the time, Hennelly had joined the office of the clergy, and was asked to prepare a report on Murtha's progress.
At the bottom of the report, which was read aloud to jurors, Hennelly scrawled notes proposing that he or others tell McKee about Murtha's past troubles, though that had not been the past practice in the archdiocese.
"Not sure if Hank was informed of Michael's file, but we (they) did not inform pastors," Hennelly wrote.
Murtha is no longer in active ministry. Two years ago, Cardinal Justin Rigali petitioned to laicize him.
Earlier Wednesday, jurors heard a former student at St. John Neumann High School in South Philadelphia describe how an archdiocesan priest stalked him, had him removed from a class, locked him in a conference room, then touched his leg and pressed him to talk about homosexuality.
"I told you I'd find you," the Rev. Francis Trauger allegedly told the boy, then 15, in 1991.
The priest ordered the boy to kneel and unzip his pants, but their encounter abruptly ended when a faculty member began banging on the door, according to the former student, now 36.
Trauger is one of nearly two dozen priests who are not charged in the case, but who prosecutors say jurors need to hear about to understand the archdiocese's long-standing practices in responding to sex-abuse allegations.
Common Pleas Court Judge M. Teresa Sarmina has rejected defense arguments that many of the cases are outdated, irrelevant, and could unfairly prejudice jurors against Lynn.
The incident described in court happened a year before Lynn became the secretary for clergy, though Lynn has said he reviewed all abuse complaints in secret church archives when he took the job.
Church officials had logged complaints about Trauger's misconduct with minors as early as 1981, according to a grand jury report released seven years ago. He was permanently removed from the priesthood in 2005.
The witness, whose name is being withheld by The Inquirer, said he was a short, scrawny sophomore when he noticed Trauger in a Center City bookstore in the spring of 1991. The teen was wearing a Neumann jacket and looking at gay pornographic magazines when Trauger approached him, he said.
Dressed in black but without his clerical collar, Trauger mentioned that he was a priest, though the teen didn't know him, he testified under questioning from Assistant District Attorney Mark Cipolletti.
Trauger demanded to see the magazines the boy was clutching. He also wanted his name, the witness said. The boy refused to tell him.
"Don't worry, I'll find you," he recalled Trauger saying.
Weeks later, the man said, he was pulled from class one afternoon and found Trauger waiting in the hallway.
Trauger told him he had approached school administrators, who were priests of an independent religious order, and said he was trying to find a former pupil of his. They let him review student ID photos until he found the boy.
Trauger kept him in the locked room for at least an hour, the man said. He was freed when a faculty member who had been looking for him banged on the door.
Trauger told the boy he knew where he lived, the names of his parents and siblings, and where his nieces and nephews went to school.
The next day, the school principal and vice principal, alerted by the faculty member, came to the teen's home to discuss the incident with him and his parents. More than a decade passed before an archdiocese investigator contacted him, in 2003, to arrange an interview about it, the man testified.
During cross-examination by Lynn's lawyer, Thomas Bergstrom, the man acknowledged he never met or had heard of Lynn until recently.
Contact John P. Martin
at 215-854-4774 or email@example.com, or follow on Twitter @JPMartinInky.
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