Yes, the San Diego concert is the same one as the PJ California Concerts, vol. 2. The Fresh Sound box does not include the quartet items.
All the available alternate takes of the studio sessions were in the excellent three LPs series 'Mainstream of Jazz', vol. 1, 2 and 3 that came out on EmArcy Japan in the mid 80s. The material was researched by Kiyoshi Kayama.