To remain in close proximity to the sources of his academic research and performance, focused primarily on the organ culture of northern Europe, Johnson remained in Europe and was enrolled at Oxford University (Christ Church College) from 1978—studying with Denis Arnold, Anthony Baines, John Caldwell, Simon Preston, and Alan Tyson, receiving the Doctor of Philosophy in Music in 1984, with a dissertation on 16th- and 17th-century organ tablatures.
During this period, Johnson also performed with the Groningse Bachvereiniging,[6] specializing in historic choral performance practice, and with the baroque chamber ensemble, Fiori musicali, [directed by Thomas Albert (baroque violin), with Niklas Trüstedt (viola da gamba), and Stephen Stubbs (lute)], recording for Radio Bremen and Récreation Records.]
[7] Rather than an exhaustive manuscript study of a single source, which was a common research practice of the period, Johnson's dissertation looked broadly at a complete corpus of 58 related manuscript tablatures (as well as 9 printed tablatures) and may be considered an early example of the data-mining methodology often used in the field of Digital Humanities, made possible by early word-processor technology.
He was an early advocate for first-year-experience education at DePauw, and taught many years in that program—both in January-term as well as semester-long courses, both in Music as well as non-Music topics.
During his early academic career, Johnson's research concentrated on the historic North-European pipe organ, its literature, as well as its unique tablature notation, about which he published.
He was an organist/choirmaster for numerous congregations, often spearheading projects for new organ installations, including First Presbyterian (Huron, OH),[22] Calvary United Methodist (Brownsburg, IN),[23] and St. Andrew's Episcopal (Greencastle, IN).
Despite his research in the North, Johnson lived in the southern city of Chennai, studying carnatic singing and participating in the 155th Tyagaraja Aradhana in Thiruvaiyaru.
With funding from the ASIANetwork, in 2003–2004, he involved a small team of DePauw School of Music students[27] in a digital-humanities project in Chennai, India, gathering data from over 2400 compositions in almost 300 live concerts during the Madras Music Season, revealing the relatively small number of ragas actually used in performance from among the thousands of theoretically-possible ragas.
[28] In 2008, having served as Dean of the School of Music at DePauw since 2006—during which time he oversaw the move of the School of Music into the new Joyce and Judson Green Performing Arts Center—Johnson took a leave of absence to become executive director of the Thomas J. Watson Fellowship (New York, New York)[29] Johnson was the last in a series of sixteen alumni directors, each of whom served two- or three-year terms, administering the same organization that had funded them, post-baccalaureate, early in their careers.
He was executive director during the Great Recession in the United States, and oversaw a needed reduction in the number of Watson-affiliated colleges and universities.
At the end of his term, he assembled previous Watson directors to evaluate how the fellowship program had evolved during more than four decades of serial leadership.
He led the institution, home to the Murtogh D. Guinness Collection of Mechanical Musical Instruments and Automata, to adopt a new mission that explores intersections of "art, sound, and motion," leveraging that collection of historical technology to examine contemporary topics such as robotics, music-on-demand, binary coding, artificial intelligence, and video gaming.