He also pursued his graduate work at the University of Notre Dame in Indiana, and there earned a Master of Arts degree in liturgical research in 1973.

[3] He received his episcopal consecration on January 27, 1983, from Archbishop Edmund Szoka, with Bishops Harold Perry, S.V.D., and Arthur Krawczak serving as co-consecrators, at the Cathedral of the Most Blessed Sacrament.

[3] In addition to his duties as an auxiliary bishop, Cooney was the founding chairman of the Archdiocese's Church in the City Task Force from 1983 to 1990.

He also served as liaison to the Catholic Chaplains of Region VI (Michigan and Ohio) from 1987 to 1991, and a member of Board of Directors for Notre Dame Liturgical Center (1987–1991) and for the Pontifical North American College (1988–1994).

[5] After the Detroit Free Press reported on the situation in 2003, he said that Shirilla had made "some errors in judgment" but was "no threat to the well-being of our children," only to suspend him two weeks later.

From 1993 to 1998, Cooney was a board member of the National Institute for the Word of God and of Sacred Heart Major Seminary.