I absolutely agree that the material from this era totally deserves more quality and detailed package. 'Fun City' is pretty good, but like you mention, it seems like many, if not all the tracks, are rips from vinyl or casette and not the original master tapes.
That material definitely cries for a good remastering too, as well as Second Wave. That album particulary is well produced, but suffers from poor mastering. I recall the co-producer also admitting that on this board a few years ago.
The Filet of Soul 2017 release made me very excited that there'd be more cool J&D releases in the pipeline. In my opinion they deserve a boxset with all of their recorded material (both together and solo, including re-record and live versions) from everything from 58-onwards. Original mono (when available) mixes, paired with new stereo remixes. All of the odds, ends, outtakes, and alternates found in the "Collectors Series" we all cherish, Dean's somewhat recent recordings with the Bamboo Trading Company, and anything else that still sits in the vaults.
The Beach Boys just got their 'Feel Flows' boxset which did wonders for the band and the brand, so I think there would definetely be an appetite out there for a detailed, meticulously assembled, career spanning J&D release.