I'm cobbling together a test scenario which is a bit less populated and a bit more straightforward than Chariot of the Gods, as I haven't GM'd for ages and the players are new to the system. One thing I'm finding useful is putting potential Events in with (my admittedly less detailed) Location descriptions, so if the players (or me) stall at any point on the map something can happen for them to react to in order to give a bit of a jumpstart.
Attaching Events to Locations is an excellent idea.
From a GM perspective, consider working backwards. What does your endgame look like? Do you want to include the Sotllio
[Prepared to be Boarded]? Do you want to go the Inflected/Abomination route [The Infection Spreads]? Do you want to go Adult Neomorph stalking route [Hunter and Prey]? I'd pick one, and as the GM, really hammer home that intended outcome.
Be wary of Act III Events that don't always work out as intended: [Mutiny!] and [Contamination Protocol]. [Mutiny!], as written, is Clayton-centric, which if an NPC, requires the GM to put in some work. As for [Contamination Protocol], I got push back from my players saying it's a little too convenient (Spoilers) that even after defeating Lucas, he uploads himself to the mainframe of the Cronus
and triggers a reactor overload anyway. "What was the point of trying to save the Cronus
for the last two Acts if the GM was just going to blow it up one way or another?" Seemed to be a forced conclusion, though that might have been the fault of how the GM (me) narrated it.