Writing the scene where Argos explains the whole story about the Argoi will be extremely difficult because of all the variation associated with how the player solved the puzzles and treated Argos so far. It'll most likely have to be a collaboration between Nemo and I, because I know for sure I can't do it alone. There's also a bit of Luke content I've been meaning to write for a while, it will be a juicy challenge (of the non-sexual variety).
Overall, I'd say that the most challenging thing going forward will be making sure the external plot mixes just right with the romance story. What's going to happen is that in the next main chapters the MC and Asterion will be told about a task they would benefit from accomplishing, and then you'll be left to your own devices to finish it on time. After that the main story will focus a lot on the relationship between Asterion & the MC, while the management stuff deals with that task. Getting these two to mix narratively and mechanically, and have them lead up to the end of the game, will be a challenge. But I think we can manage.
Everyone knows where the story is going, but whoever's the writer for a given part is always thinking ahead so they're probably a few steps more advanced in what they know is going to happen. And, you know, while we have a rough idea of what's going to happen we are kind of like a jazz band, we adjust on the fly to hit the rhythm we want. So there're always a few surprised here and there.