Now he has the Mustangs ready for the Hawaii Bowl on Thursday against Nevada, their first bowl game in 25 years -- in a stadium he knows well.
Jones has resuscitated an SMU program that had long been mired in futility after being hit with the NCAA's death penalty. Around here, he's known for turning around a once-dismal Hawaii program and guiding the Warriors to the Sugar Bowl before abruptly leaving for Dallas.
The Mustangs (7-5) finished 1-11 the past two seasons, including their first under Jones, but can wrap up the year with a win like they did in the 1984 Aloha Bowl.
"It's just nice to finally put an end to the death-penalty talk," linebacker Chase Kennemer said. "It's all you hear about. So it's special to be on the team that finally put an end to that and I couldn't think of a better destination than Hawaii to go to our first bowl game."
The program that produced Doak Walker, Don Meredith and Eric Dickerson was discovered in 1987 to have paid players, then lied about it in a cover-up that included a former Texas governor. Because the school already was on probation, the NCAA shut the football program down for the season and school officials chose to sit out another year before restarting in 1989.
They won two games that first season and have had nine seasons with zero, one or two wins.
Nevada (8-4), which finished second in the Western Athletic Conference to Boise State, is trying to break a drought of its own. The Wolf Pack are making their fifth straight bowl appearance, but have lost their last three.
"It's cool to go to bowl games and it's a great experience, but it's time we win," Nevada lineman Alonzo Durham said. "We're overdue."
Their last bowl victory, like SMU, came in Honolulu. A missed extra point lifted Nevada to a 49-48 overtime win over Central Florida in the 2005 Hawaii Bowl.
"I watched them hold up the trophy. I remember it like a still frame in my mind," said Durham, who was a redshirt freshman on that team. "Those guys were so excited. I just said, 'I want to be a part of that. I want to know what that feels like."'
Thursday's game could end up being a high-scoring affair with offenses that feature names suitable for an old John Wayne film -- the pistol versus the run-and-shoot.
Nevada has the nation's No. 1 rushing attack that averages 362.3 yards, and is the first team in NCAA history to have three 1,000-yard rushers. But the Wolf Pack will be without two of them in running backs Vai Taua and Luke Lippincott.
Taua, who led Nevada with 1,345 yards rushing, is academically ineligible. Lippincott, who ran for 1,034 yards, is sidelined with a toe injury. Nevada will also be without safety Duke Williams and linebacker Andre Davis for undisclosed violations of team rules.
Nevada coach Chris Ault announced Williams' suspension and Davis' dismissal on Wednesday.
"Like we told the kids, sometimes the flag is dropped and sometimes you have to pick it up and run with it. That's what we expect them to do," Ault said.
He said the Wolf Pack will not change what they do or call more plays for quarterback Colin Kaepernick, the team's lone remaining 1,000-yard rusher. The backups will need to pick it up.
"Those guys got to stand up and play," Ault said. "Your chance has come. What a thrill. Playing before a national audience Christmas Eve, this is great for you guys and I think they're excited. I don't think they're getting much sleep, but I think they're excited."
Regardless of who is running, SMU will be challenged by misdirection, bootlegs and motion.
"They try to get your eyes wrong, so if one time, one guy goes to the wrong gap, they're out the gate," Kennemer said.
SMU, meanwhile, features a heavy passing attack behind a young quarterback and sure-handed Emannuel Sanders, its career leader in receptions, touchdown catches and yards. The Mustangs also have Shawnbrey McNeal, the first running back under Jones to rush for 1,000 yards.
As former conference foes, Jones and Ault know each other well. Nevada may be the WAC representative, but this was Jones' house and bowl game. He's 15-1 at Aloha Stadium since 2006, and is 3-1 in Hawaii Bowls with three straight wins.
"I'm looking forward to being on the same sideline I used to be on and the same locker room, too," he said.
Jones actually set the Hawaii Bowl as a goal for his club since the first practice of the season. It was a promise he made to his friend Frank Gansz, who was the special teams coach until he died in April.
Local fans, bowl officials and ESPN didn't get the Hawaii-SMU matchup they were hoping for, with the Warriors falling one win shy, but the Mustangs are relishing every moment.
"Come Thursday, when we come down there for the real thing, it'll probably more emotional," Jones said.