After some further use of Manuscripts to try to write a scientific journal publication, I have decided to put it aside. I encourage the team to continue its development. Manuscripts is a promising piece of software that I will certainly want to use in my future work. Unfortunately, it is not yet stable and reliable enough. I spend too much time in frustration re-doing simple actions that do not work consistently, discovering bigger things that do not work well if at all, and handling nuances in function that do not jive with my view of streamlined workflow. I might echo the sentiment stated elsewhere ... Perhaps this is the time to freeze the expansion of new features and fix the existing package to be rock solid ... or at least worthy of being called a reliable package to use even if it is still just at a basic level of design.
I look forward to coming back later to see where Manuscripts is standing.