Since I last posted, I've gotten the scenario to the point where it can be run. I've GM'ed the scenario twice and am sharing the problems and feedback we found:
In game A I was excited and pushed my players to act more than was healthy for an atmosphere that was supposed to be tense. I re-wrote the encounters to encourage the GM to describe hooks without asking for checks - before, I required players to make an observation check or miss the encounter and that sucked. With this new way, I point stuff out in the environment and the players pick what to dive into without direct prompting.
I learned to add more details to flesh out player interactions. The maps and locations are very helpful - I don't think any edits are needed for them.
I need to clarify the ending conditions for the scenario. The players did really well and figured out how to fight the monsters, but one of them managed to get word out to one of the governments about the monsters, so the final fight was against a black ops squad of androids with smartguns.
I have several of these 'twist' scenarios in mind, and I need to incorporate that into the mission structure.