Ziba: I think I've seen a tip about starting the mission in your spacesuit. Then when the mission ends all your ships will be intact, and you'll end up in a Buster. Free ship! I wasn't sure of when I should do this when I started, so I didn't do it.
And it doesn't matter what ship you start in since you get different ships for the different tasks as you play the mission. I got killed once as well in the final objective, but that was mainly because I didn't know what to do and ran out of time. You'll never use your starting ship during the mission.
Finally, regarding my own status: As I've been playing for a few more hours now after completing the last mission, I've killed 5 or 6 Novas that were chasing me, and 6 Busters as well (all of them in Boron Space). I think I had Federation Guardian 86% earlier (+/- a couple), but now I have 24%...
Oh well, what is done is done. I was warned in this thread after all (although it didn't say anything specifically about this in the first post). Just hope there aren't any more Argons after me. Things are finally back to normal, and my UTs have started trading in Paranid space.