Later, in 1957 and 1959, he studied with Cage, who encouraged him to follow his desires and use traditional instruments rather than electronics or newly built instruments. Unskilled in carpentry and finding electronics unreliable, Johnston struggled with how to integrate microtonality and conventional instruments for ten years. He also struggled with how to integrate microtones into his compositional language through a slow process of many stages. However, since 1960 Johnston had almost exclusively used a system of microtonal notation based on the rational intervals of just intonation, what Gann describes as a "lifelong allegiance" to "microtonality". Johnston also studied with Burrill Phillips and Robert Palmer.