[11] From 1997 to 2000 Vaughn was Chief of the Operations Division at National Guard Bureau,[12] and he was assigned as the Army's Deputy Director for Military Support to Civil Authorities from 2000 to 2002.

[14] In September, 2002 Vaughn was assigned as Deputy Director of the Army National Guard, succeeding Michael J. Squier, and he served until November, 2003.

[17][18] One of the initiatives that operated during Vaughn's tenure, the Guard Recruiting Assistance Program (G-RAP), was later the subject of controversy and investigations.

[20] As a recruiting tool, G-RAP was widely viewed as a success, because it helped the National Guard meet or exceed its annual end strength goal of 350,000.

He graduated from the United States Army War College in 1994, simultaneously receiving a Master of Public Administration degree from Shippensburg University of Pennsylvania.

In 2010 the Army National Guard's GED Plus program, which enables recruits to complete their high school equivalency before beginning their initial training, was named for him.