5) If it comes to a stop, just load your last savegame and try again. No amount of waiting, blowing up ships or anything else will make the mission proceed from here.
Wandering off and coming back again seems to work too.
I tried that a few times, but when I came back no ships appeared. Granted I didn't try this very many times, so I have no idea what the success to failure ratio is for the "wander off" method compared to what I described above.
It's possible I didn't wander far enough away, or stay away long enough. I was able to get through the mission eventually, so hopefully everyone else can too. It's a shame to have to skip over that mission because it's a pretty important plot element.
I just finished the game yesterday and it's a blast. The only complaint I've ever had about IW2 is that Act 3 is pretty linear and doesn't do much to incentivize exploration in the Gagarin cluster.
Oh and Ravenger, maybe you know the answer to this question that has ALWAYS bugged me about this game:
MINOR SPOILER WARNING:
How in the world is your base + two megafrieghters supposed to squeeze through that jump accelerator? The base alone is at least 3 times the diameter.