It is an ambitious undertaking for sure, and I definitely went a little overboard with choice options. Since releasing the last story update, I've been working to streamline how I reference everything. I've learned programming tricks I didn't know about early on that helps with that.
Tracking things like who knows who, positions, etc. actually isn't too difficult, it's mostly the intricacies of relationship choices that can be complicated. But that was the purpose of the most recent story update (and why it took so long). It lets both the player and the game set a relationship goal for everyone so I can just write a few versions of each scene going forward, be them romantic, sexual, both, or just friends with a guy.
I'm pulling threads together even further in the next story update to narrow down to a few distinct paths that cover a lot of scenarios. Part of that involves focusing each update on just a few guys rather than everyone at once. Other guys will still appear, but not in a way that has me juggling 16 full paths all happening simultaneously.
As for threesomes, it's not gonna be a free-for-all where you can use any combination of people. There are specific scenarios that are already planned out. So not quite as unmanageable as it may seem!
Anyway, all that to say I've definitely been adjusting plans, implementing systems, and learning skills to make it all more manageable. It's still a lot of work, of course; I would definitely like to find ways that other people could help. I have to do all the writing, of course, but assistance with things like initial scene setups for CGs and game testing would be welcome.