So that's to say that
I can't do much of anything more because the technical issues render the completion of that sidequest moot?
No, I don't think that sidequest is required for much of anything (though it is very useful), the problem is that all global variables in your save file are completely butchered, meaning stuff that isn't triggered could be set to on, and stuff that should be triggered as on, isn't. This very likely means that you
can't do certain things in the post game because it's in the wrong state.
You can already see that in the experimental code to spawn rupees is running, even though it was a feature that I scrapped. A lot of it is probably harmless, but I can't really guarantee anything, and it's likely some content is permanently locked off due to it.
In addition, does the lack of address to my questions about those rooms in Fall of Stones mean that FoS is post-game content, for which I'm on my own?
The area can be accessed before the post game and even potentially completed to some degree, but as you are aware since you have completed the main segment, it's not required.
It was not really my intent to not answer questions about the area specifically, it's just the save file corruption was more pressing.