There's an old interview (1999) with Franz's daughter Karen that can still be read, and it provides some interesting insights into the evolution of FJ's work with Gene's projects and there is a timeline of events as well, based on communications and other things she saved over the years. Karen came to feel, over time, that a lot of the souring of the relationship came from Roddenberry's end, as he resented the fact that he couldn't persuade FJ to initially use Majel Barrett's business (Lincoln Enterprises) to be the source of the Starship Plans and Technical Manual, as that would have allowed Gene to directly profit from their sales. Part of the problem seems to have been that, from FJ's perspective, it was not entirely clear who actually owned the rights to the series (as Gene had created but Paramount owned it, if I understand correctly, which is why they helped Ballantine publish the TM independently of Roddenberry). There were a lot of miscommunications and mixed messages flying around, compounded by the then hectic production of The Motion Picture that was evolving. The whole story is fairly complex, and it is indeed unfortunate that FJ and Gene didn't have a more amicable relationship.