He was also a member of the band Spatula. Formed in 1993, the instrumental indie rock trio issued a total of four albums between 1994 and 1998. Johnson's early production and engineering, and his penchant for home recording, are present in the band's discography. From 2000-2004 he was also a member of Shark Quest, who issued three albums for Merge. The real first evidence of his earlier guitar influences can be heard on recordings made with the group Idyll Swords, a trio of guitarists that also included Dave Brylawski and Grant Tennille. Solo Guitar, Johnson's debut offering from 1999, was, however, a far cry from the sound of his forebears. Instead, it was a vanguard album that expressed an interest in getting unusual sounds from the instrument rather than displaying his performing style. An album of free improvisations on acoustic, electric, and prepared guitar, it was issued under the pseudonym Ivanovich on Amish Records. There were so many sounds on it that several critics thought it had been made by a band, not a lone artist. Possessing a Catholic range of musical interests, Johnson's explorations also included classical Indian instruments, banjo, and synthesizer. In 2004, as Pykrete, he produced and played on a free improvisation session with oboe player Carrie Shull and Czech toy instrument virtuoso Martin Klapper. The album Over Hylaster appeared on his own Cirrus Oxide cassette tape label. In 2006, he released No More Love to Give in collaboration with Southern Man on Phaserprone.
In 2003, Johnson scored his first feature-length film with the documentary Tobacco Money Feeds My Family, a joint production between the University of North Carolina TV and PBS.
Johnson also incorporated just intonation or steel guitar with electronics into his experiments, such as Stalwart circle, wavering canton (2006). He also composed for other instruments as well. Notable works include Fluvial Cortex - for trombone and electronics (2007), Stoa Poikile - for small ensemble of non fixed-pitch instruments and 96 resonant band-pass filters (2008), Seven Orbits - for solo zarb, composed for zarb player Luigi Marino, and Meet me by the pleroma – for violin, long string duochord, slentem, and electronics, both from 2009. He completed an MFA from Mills College the same year.
In 2011, Johnson issued A Struggle Not a Thought, on Strange Attractors, his first solo acoustic fingerstyle guitar album. It was embraced by critics and guitar enthusiasts alike for its technical acumen and the emotional and historical depth of field in Johnson's compositions. This period proved beneficial for Johnson as a soundtrack composer, too. His work appeared on the Tennis Channel's Who’s Next that year, and he scored the documentary Maria Full of Hope in 2011. In between, he released Liber Novus as Pykrete on FrequeNC. In 2013, Johnson issued the landmark, universally acclaimed Crows in the Basilica on Three Lobed Recordings. He also composed for PBS' Standing on Sacred Ground and scored the first of three seasons of A Chef's Life that year. In 2014, he scored HBO's documentary Private Violence and contributed the track "On a Slow Passing in Ghost Town" to Tompkins Square's Imaginational Anthems, Vol. 7. His experimental classical album, CJ-1 CS, was issued by Drawing Room Records in the spring of 2015. His solo acoustic fingerstyle album, Blood Moon Boulder, was issued by Scissor Tail Editions. Johnson switched gears for 2016's Velvet Arc, released by Trouble in Mind. He played acoustic and electric guitars as well as synthesizer, and used a rhythm section comprised of bassist Ben Bracken and drummer Alex Vittum, with violin by Marielle Jakobsons. The album received nearly universal critical acclaim. In late 2015, before it was even released, Johnson went into the studio and switched up his process again. Over a two-week period, he tracked another record, this time on pedal steel guitar. He returned to it between tours in the spring, arranging the raw material and adding treatments and effects. The end result was Balsams, issued by VDSQ in June 2017. Stylistically and sonically, the finished recording owed more to the sounds of Harold Budd and Fripp and Eno than the American Primitive guitar school he'd so long been associated with. ~ Eugene Chadbourne & Thom Jurek, Rovi