There was much hype surrounding the Frogs going into the 1985 season, and Wacker appeared on the cover of Dave Campbell's Texas Football alongside his All-Americanrunning back, Kenneth Davis, a finalist for the Heisman Trophy in 1984 and a leading candidate for the award in 1985. After the first game of the season, Wacker discovered that several players, including Davis, had been benefiting from a payment plan in violation of NCAA rules. He dismissed the players from the team and voluntarily reported the infractions to the NCAA, which issued stiff recruiting penalties on his team. These actions led to Wacker's reputation as a man of integrity. Fans of TCU remain bitter that the penalty heaped on TCU for the violations were severe given that the violations were voluntarily reported.
After several years of struggling due to the NCAA penalties, Wacker brought the team back to success in 1990, when the 5–1 Frogs returned to the top 25 for the first time since 1984, before slumping after a season-ending injury to their starting quarterback. In 1991, TCU finished 7–4 for their first winning season since 1984.
Wacker served as head coach at the University of Minnesota from 1992 to 1996. Although he had a disappointing won-lost record (16–39) at Minnesota, for three years his teams led the conference with academic all-conference honors.