Will straight and gay troops have to shower next to one another? Will the military have to provide benefits to gay partners, and can it afford to? And the biggest question of all: Will gays be harassed or intimidated?
It comes down to changing the culture, and top brass say they need more time. The military has been long resistant and, at times, hostile to gays, and it draws much of its 2.4 million members from socially conservative parts of the country.
"The real issues will be not what happens on the battlefield, but what happens on posts," said David R. Segal, a sociologist at the University of Maryland who has written extensively on the military's personnel policies and recruiting.
For many troops, "they don't mind suspecting their colleagues are gay, but they don't want to know for sure," he said.
Gay rights advocates say the government's efforts to overturn a federal judge's order halting the enforcement of "don't ask, don't tell" are unnecessary. They contend there were no huge eruptions of violence with the integration of women and blacks, even though the military had to contend with race riots among the ranks during the Vietnam War era.
Opponents of repeal point out that women have never been integrated into combat units. Women are still banned from many front-line units like infantry and special operations.
Advocates acknowledge that harassment will likely happen, just as it continues today with those groups. They say another aspect of military culture - following orders - will override any temptation to intimidate gays.
"If your commander-in-chief says this is the new law, then that's the way we follow it and we make it work," said David Hall, a former Air Force staff sergeant who was discharged under the 1993 Clinton-era policy.
The fate of the law remained in doubt Wednesday, as a federal appeals court temporarily granted the government's request for a freeze of U.S. District Judge Virginia Phillip's order.
The court instructed lawyers for the Log Cabin Republicans, the gay rights group that brought the lawsuit successfully challenging the policy, to file arguments in response by Monday. The judges would then decide whether to extend the temporary stay while it considers the government's appeal of Phillips' ruling that the policy was unconstitutional.
It was unclear what effect the temporary freeze would have on the Pentagon, which has already informed recruiters to accept openly gay recruits and has suspended discharge proceedings for gay service members.
Cynthia Smith, a Pentagon spokeswoman, declined to say whether the Defense Department would roll back its guidance to military lawyers and recruiters that they must abide by last week's injunction from Phillips.
It has been assumed, however, that the Pentagon would revert to its previous policy if a stay were to be granted.
Seeking to suspend or overturn Phillips' ruling leaves the Obama administration arguing against its own policy goals of repeal and against the majority opinion among the Democratic base most likely to turn out for midterm elections next month.
Allowing the courts to steer the lifting of the ban leaves military leaders feeling rushed and misled.
Nervous about forcing the change with so much opposition at the senior uniformed ranks of the Pentagon, Mullen and Defense Secretary Robert Gates devised a plan: They would back President Barack Obama's repeal plan but move slowly.
They ordered a yearlong study on how to repeal the law without hurting the military's ability to fight. Top military officials thought they had bought time to prepare the uniformed forces, spouses, families and veterans for openly gay service.
Officials who spoke on condition of anonymity because the administration's path is still uncertain said officials have never fully acknowledged that while a majority of Americans may want repeal, a majority of the uniformed military might not.
Still, gays already serve in the military, many with the knowledge of colleagues who promise to protect their secret.
It was this fact that led the top uniformed officer, Adm. Mike Mullen, to tell a stunned Senate hearing room last February that the "don't ask, don't tell" law should be repealed.
"No matter how I look at this issue, I cannot escape being troubled by the fact that we have in place a policy which forces young men and women to lie about who they are in order to defend their fellow citizens," Mullen said. "For me personally, it comes down to integrity - theirs as individuals and ours as an institution."
But even as Mullen made his case before Congress, his fellow service chiefs, including the Army's Gen. George Casey and Marine Corps Commandant Gen. James Conway, were opposed to making any changes when the military is fighting large, protracted wars with its all-volunteer force.
Underlying their concern was the military's culture.
Unlike most Americans who support allowing openly gay troops, the rank-and-file are suspected by their leaders to be considerably less permissive.
The men and women serving in the armed forces today represent less than 1 percent of the country's total population, and come heavily from rural, conservative areas in the South and the mountain West.
Among their concerns was how to effectively implement new policies for sharing close quarters and living facilities.
Military officials say privately that the service chiefs worry most about a cultural backlash and displays of intolerance that would make the military look as if it had lost control of its troops.
If the military lifts the ban suddenly, would there be attacks on gays? Would religious parents, coaches and teachers who oppose gay rights persuade young recruits not to enlist? If a platoon member says he is gay, would his comrades still support him, or would there be infighting?
Conway, the Marine Corps commandant, claims, by his own informal survey of the force, some 90 to 95 percent oppose letting gays serve openly.
"We recruit a certain type of young American, pretty macho guy or gal, that is willing to go fight and perhaps die for their country," he said.
The experience in militaries of Britain, Canada and Israel showed that allowing openly gay service members was a "non-issue, non-event," said Lawrence Korb, a former assistant defense secretary who oversaw military manpower and reserve affairs during the Reagan era.
"Britain dropped the policy within a month," said Korb, now a senior fellow with the liberal Center for American Progress. "I can't believe that people, that Obama let himself fall into this idea that we got to do a study. Just do it!"
Korb said the Uniform Code of Military Justice also outlines how people should treat each other.
According to Segal, the sociologist, the true impact of Phillips' ruling that the policy was unconstitutional depends upon how many gay troops speak out about their sexuality and how military leaders respond to any dissent within the ranks.
Segal said he expects the cultural change will happen much like it did following President Harry Truman's 1948 executive order for military racial equality.
The first test of that notion didn't come until a couple of years later during the Korean War, when the U.S. was short on troops and all-black units were proving less capable. As a remedy, the Army fielded integrated units that eventually performed on par with all-white ones.
Still, the military grappled with racial violence.
According to a 1993 RAND study, the military enjoyed a certain level of racial harmony following that war. But the "veneer of racial harmony was shattered" in the late 1960s with the rise in racial tensions throughout the country. Race riots broke out in all four services.
"We will still have to deal with hate crimes," Segal said. "Fifty years from now, we'll have to deal with hate crimes. . . . It's going to take doing it (changing the law) and good leaders who are committed to making it work.
"Once the top level says 'This is where we go,' people are going to move in that direction."
Flaherty reported from Washington. Associated Press writers Anne Gearan in Washington and Lisa Leff in San Francisco contributed to this report.