Expedition Questions

So, this is my first expedition (almost done, I think...stuck at 3/6 waypoints and super annoyingly, finished my 5th long haul exactly 1 toxic container short of finishing that milestone, so now I'm running around trying to find one more toxic container). I have a few questions, some on this one specifically, some in general for those who have done this before...

1. When exactly does the spaceship come online/become fixable? Is it once I get that last toxic container and finish all of the milestones (other than the waypoints)? (Or more specifically, when I finish the third milestone for the Expedition story mission, which is at 6/7 right now.)

2. What exactly carries over from the expedition into my main save? Do I keep units/nanites earned in the expedition (or are those automatically moving over at the time)? Do any of the items I've gathered transfer over? If they don't, should I just sell everything I've gathered/been rewarded in order to pump the units that transfer over? If they do carry over, when do those items move to the main save?

And...I think that may be it, actually. I thought I had more questions, but I guess not (or rather, they're all part of the second question).