What do you have so far? 
Sure we can just answer those questions but it's better for you if you tell us your ideas and we help you refine them.
Well, let's see...
1) There is an event with the Argo docking and after 30 secs the IFF changing to friendly. I tried "is-event-true-delay" but it didn't work.
2) It is clear until the point of "when;not;is-destroyed-delay", but I am just unable to add a point of reference, since I am unable to insert the part on page 2 since I cannot add "has-arrived-delay" at the "true" field, and no matter where I try to add or insert an operator, I am unable to recreate the "arrival of reinforcements" thing.
3) My idea was that if the player leaves the field before the very first event, then he gets the AWOL one. Now I suppose that I should add a "Return to base" directive at the end of the mission but I still have no idea what to do with those events (probably an "is-event-false-delay").
So, these are my ideas.
In the middle of this brainstorming, I created my very first cutscene and I am quite proud of it
