1: They won't raid, but you will still get pirate activity modifier.
2: With Nexerelin, factions won't attack you, if you have positive reputation with them, but it also adds invasions, satbombings and random reputation drifts. If you're bored with normal gameplay, I would recommend it, but if you're doing fine, then you just have to endure expeditions. Free money comes with risks.
3: Independents never send expeditions.
4 & 6: Pirates and Pathers respawn indefinitely. Vayra's Sector mod changes that, but it also changes many other things and I'm not sure you can configure it just to change that one thing.
5: No.
7: There's no story in the game. There are only two quests in the game and they are very simplistic.
8: In-faction supply decreases upkeep, up to 50% upkeep reduction at 100% in-faction supply for all commodities.