I went to the order HQ and the storyline seems to resume just fine.
As for the tradelanes interruptions, I know it's the way the game work, I was just laughing a little, but it's nice to know about the formation trick.
Capturing pilots is what I intensively did at the beginning. As soon as I got a decent ship, I parked it in front of the junkers base and destroyed all the incoming enemies until my cargo got full of pilots. That got me 15 millions quite quickly. I think the rogue base in California would be a super place to do the same since it is a hornet's nest of hungry rogues. But I'll be fine as a trader for some time.
To tell me there is a rewarding bonus mission is nice, but it's not much of a hint, would you be kind enough to tell me more, like the system where I should look for it?