At Yale, Daugherty wrote his dissertation on the relationship between the music of Charles Ives and Gustav Mahler and the writings of Goethe and Ralph Waldo Emerson. He worked closely on this dissertation with John Kirkpatrick, who was the curator of the Ives Collection at Yale and gave the 1938 premiere of Ives’ "Piano Sonata No. 2: Concord Sonata". Daugherty also continued his interest in jazz where he worked with Willie Ruff and directed the Yale Jazz Ensemble. It was Ruff who introduced Daugherty to jazz arranger Gil Evans, who, at that time, was looking for an assistant. For the next several years, Daugherty traveled by train from New Haven to Evans' private studio in Manhattan. Daugherty helped Evans organize his music manuscripts and complete projects. The most notable project was the reconstruction of the lost arrangements of "Porgy and Bess", which was originally used for the 1958 recording with Miles Davis.