I think that is a really good idea, and, despite my rude words, I want to say you have most of the pieces at hand already, just try to boil the characters and the content down to the essence of what this VN started as. The first release you did was, arguably, the best iteration of the game. Expand on interpersonal, believable interactions (you can do that by basically using what you dub the best parts of the Desire/Liv relationship & interactions you already wrote, while cutting out the stuff that's just there to have all the relationships & characters in 1 story somehow)
Then, if you feel like it, do the same with the content related to Megan. As someone wrote before: Make sure there is more than 1 ending, cause otherwise the player decisions feel pretty much superfluous. If multiple endings aren't your thing then, at least, make it so that player decisions have an important impact on how scenes play out. Otherwise just cut them completely, which would also be fair enough, branching stories are really challenging to bring to life.
In regards to the sandbox thing: I'm sure some people won't like it, and I can see the reasons why, so, just my idea, to not make that feature a chore 1st of all don't make it too overbearing, yes, pacing of the VN is a bit rushed, but that doesn't mean it would be great to mix that with, e.g., 50% repetitive actions just to make it feel longer (I'm sure you know that, though). Make sure the things the player can do outside of progressing the story aren't too convoluted to keep track of, aren't just repetitive "click X times" things but maybe use the "downtime" as an opportunity to cast some more light on the characters you keep around, turn some of the scenes you already wrote for the VN into moments that happen during the "sandbox" part...just some ideas, of course.