But nearly a quarter-century since the fire, Lee, now 79 and serving a life sentence, could be on the verge of release because of recognition by courts that the science of arson investigation has changed dramatically - and that those once-classic signs of an intentionally set fire are now known to be little more than old wives' tales.
Lee is among a handful of Pennsylvania inmates - including Daniel Dougherty of Northeast Philadelphia - seeking their freedom because of the evolving fire science. Convictions already have been overturned in Michigan, Indiana, California, and Massachusetts, according to Marissa Bluestine, legal director of the Pennsylvania Innocence Project.
Nationally, there has been widening discussion about what could be hundreds of arson convictions built on now-discarded beliefs of what constituted an intentionally set fire.
"The legal system is beginning to wrestle with what we're going to do about those cases," said John Hollway, associate dean at the University of Pennsylvania law school and executive director of the Quattrone Center for the Fair Administration of Justice at Penn.
This month, Lee won his most significant legal victory when a federal magistrate judge in Harrisburg recommended that he be retried or released. A U.S. district court judge is reviewing that recommendation and could rule soon.
"It's plausible to think he could get out soon," said lawyer Peter Goldberger, who has represented Lee for 14 years.
On Friday, Monroe County District Attorney E. David Christine Jr., who handled the trial two decades ago, and an assistant prosecutor, Bradley Schmidt, filed objections to the magistrate's report, saying that Lee "has not been exonerated by the new fire science evidence" and that the report "underplayed the strength" of the prosecution's case. Schmidt said last week that he doubted the case could be retried after so many years.
Later Friday, Goldberger filed a motion for bail, calling the prosecution's objections "insubstantial."
No one disputes that Ji Yun Lee, a student, was mentally ill. She had been hospitalized for her emotional difficulties but had stopped taking her medication before her death. Earlier that month, she wrote in her diary that she was sad and wanted to kill herself. And the day before her death, police were called to the Lee home in Queens because she had been throwing items out of the house, according to testimony at her father's 1990 trial.
The Lee family's pastor suggested the trip to the religious retreat, with its small group of cabins in the rolling hills of Stroud Township. There, a pastor held a prayer service in which he placed his hands on Ji Yun Lee and ordered the devil to leave her, but the young woman struggled and became violent. The pastor needed help to subdue her, he later told jurors, news accounts show.
Finally, according to testimony, Ji Yun Lee and her father retired to their rooms in the cabin.
The fire was reported at 3:18 a.m.
Christine told jurors that Han Tak Lee had killed his daughter out of frustration with her escalating mental illness. But the key trial testimony was the police analysis of the fire scene.
Fire investigators said there were burn patterns indicating eight or nine points of origin, as well as finely cracked - or crazed - glass, all sure signs back then of an arson.
One investigator also cited traces of a flammable liquid on the elder Lee's shirt and pants, and said those materials matched remnants found on a glove and jug at the scene.
Lee's trial lawyer tried to convince the jury that his daughter must have set the fire to kill herself. Lee didn't support such a defense because suicide is forbidden in the Korean culture. But with the help of a translator, he told the jury he did not set the fire.
It took jurors 41/2 hours to convict Lee. He lost his appeals in the state court system, and a federal judge rejected his request to challenge the scientific validity of the conclusions reached by the fire investigators.
But in 2012, the U.S. Court of Appeals for the Third Circuit concluded, in a precedent-setting decision, that Goldberger had presented a "convincing claim of innocence" on Lee's behalf and that Lee deserved a chance to challenge the conviction based on the evolving science.
Goldberger called nationally recognized fire investigator John Lentini, who had long been troubled about the evidence used to convict Lee.
In a 1999 article for a fire-science publication, Lentini wrote that Lee's conviction was the "ultimate triumph of junk science" and argued the fire was mistakenly categorized as arson. He found numerous problems with investigators' conclusions, including the assertion that more than 60 gallons of fuel oil and gas had been used to start the fire, though no trace of either was found in the cabin.
After the Third Circuit ruling, Lentini analyzed the clothing, glove, and jug, concluding that, contrary to what investigators had testified, the specimens did not all contain the same mix of hydrocarbons. While the shirt had traces consistent with gas or fuel oil, the pants had no petroleum traces and the jug and glove had traces of fuel oil but not gas.
U.S. Magistrate Judge Martin C. Carlson concluded that most of what the jury heard was based on a flawed analysis of the scene and "it is now uncontested that this fire science evidence - which was a critical component in the quantum of proof that led to Lee's conviction - is invalid," he wrote.
Carlson also found that Lentini's analysis of the shirt, pant, jug, and glove undermined what was left of the state's case. He said the analysis showed the substances all turned out to be different - unlike what jurors had been told.
The judge also noted that the state had lost the original chemical tests of the items.
Since then, Carlson wrote, "there has been a revolution in fire science."
The first shadows of doubt had begun in the 1980s, but they weren't widely accepted until after Lee's trial, with a growing recognition that the classic signs of arson could no longer be considered proof. Scientists learned this largely by a practical approach - starting fires and watching them burn.
Fire marshals had thought, for example, that fires begun with flammable liquids reached very high temperatures - higher than an accidental blaze. Research showed, however, that the temperature is actually affected mostly by ventilation.
Finely cracked glass - like that found at the scene of the fire that killed Ji Yun Lee - also was once viewed as an indicator of a rapid heating caused by an accelerant. Scientists now see that the "crazed" surface is merely the result of quick cooling when hot glass is hit with water.
Burn patterns on a floor - much like those found in Lee's cabin - were another classic sign of an accelerant. They still are, but now investigators know not to read too much into those patterns because they also occur when a room becomes engulfed in flames, an event known as "flashover" - even in an accidental fire.
It now seems likely that the cause of the fire will never be known.
Han Tak Lee, incarcerated at State Correctional Institution at Houtzdale in central Pennsylvania, hopes to be exonerated. His wife stood by him through the trial. They later divorced, but she believes in his innocence, as does the New York Korean American community, said Kyung Sohn, a friend of Lee's.
He said Lee had come to the United States in search of the American dream, and was doing well as the owner of a women's clothing store in Manhattan. Then came the fire.
"He lost his whole life," Sohn said.
Chris Chang, a New York radio host, said Lee has long maintained that much of what he told police was lost in translation, and that there was a lack of understanding about Korean customs, especially the public stoicism expected of men even in the saddest of circumstances.
"It's a tragedy," Chang said.
In and around Stroud Township, the fire is mostly a dim memory.
Warren Dean, 59, a retired park ranger who lives less than a quarter-mile from the retreat that now belongs to another Christian organization, said he recalls the sounds of breaking glass and loud voices early the morning of the fire. From time to time as he drives past the retreat, he said, he thinks of the young woman who perished and wonders what really happened.
"Perhaps no one will ever really know," Dean said recently in his front yard. "It's a shame."