On the subject of GUI one idea I had was that when you click on the compounds summary at the bottom (whatever that will look like) the game pauses and you the screen is filled with the CPA diagram (see here). Each compound box could show how full you were of that compound and each link could show which processes are ongoing / happening. We could have it that when you click a link it toggles that process on and off. And when you click a compound it get’s added (or subtracted) from the compounds quickbar.
I think that would be a good way of explaining how all the compounds are related and providing a control panel for them all in one go.
Anyway just an idea. I am really not a design guy.