The German Modding Handbuch is quite useful with regards to creating the alien and precursor flights you want but not much else (the icon change section is self-explanatory, doesn't need a manual). There's plenty of berserks in the Border systems imho, but you can add them to your custom systems if you wish. It's not just flights, don't forget the portals connecting it with other systems

For ship stuff look at Carcasses.xml and ShipDescriptions.xml. Adding stuff to trade is likely in IniTradeSystem.xml.

Edit:
On an unrelated note, was just digging through the perkDispatcher script since there were a few things bugging me. Turns out I was right, the values and descriptions don't match. Meh.

Missile skills damage:
- Base, Missiles_Rockets, Missiles_2, Missiles_3, Missiles_4, Missiles_5, Elite, Lone Wolf (huh wtf):
base = 0.95
Missiles_Rockets += 0.05 = 100% (i.e. the stated damage)
Missiles_2 += 0.05 = 105%
Missiles_3 += 0.1 = 115%
Missiles_4 += 0.15 = 130%
Missiles_5 += 0.15 = 145%
Elite += 0.2 = +20%
Lone Wolf += 0.1 = +10%

However, descriptions (from m_perks.loc) tell a different story:
Missiles_2 = 5% (correct)
Missiles_3 = 25% (incorrect, script shows it is 15%)
Missiles_4 = 50% (incorrect, script shows it is 30%)
Missiles_5 = 45% (ironically correct, presumably bonus is lower to compensate for anti-jamming bonus - except script proves this is false)
Elite = 25% (incorrect, script shows it is +20%).
Lone Wolf = 0% (incorrect, script gives 10% bonus even though description says no bonus)

Not a huge deal since missile damage is quite overpowered already (hello massive blast damage) but I'd just like to point out that the values are described wrong.

Another gotcha: if you design a new skill tree and skip the lower skills and jump straight to the higher skills, e.g. base then straight to Missiles_4, and not giving Missiles_2 and Missiles_3, you get different values:

• Missile_4 gives 30% damage bonus due to: base (0.95) + (Missiles_Rockets, 0.05) + (Missiles_2, 0.05) + (Missiles_3, 0.1) + (Missiles_4, 0.15)
  = 0.95 + 0.05 + 0.05 + 0.1 + 0.15
  = 130% modifier (aka 100% @ full base damage + 30% bonus)
• But skipping the low level skills only gives you: base (0.95) + (Missiles_Rockets, 0.05) + (Missiles_4, 0.15)
  = 0.95 + 0.05 + 0.15
  = 115% modifier (aka 100% @ full base damage + 15% bonus)

How to fix this is simple, edit the script to give a straight assignment to the modifier value (amplifier = xx) instead of an increment bonus (amplifier += xx). Do this for the "chained" skills, i.e. Missiles_2 to Missiles_5. Elite is fine as an incremental bonus - it makes sense, a missile-specialist Elite pilot will still be better with missiles compared to a piloting-specialist Elite pilot. Note that you should do checks that give assignment modifiers first before checks for increments, e.g. check for Missiles_3 first before checking for Elite. Otherwise the increment from Elite would be overridden by the assignment from Missiles_3.

Haven't exactly decided how I should fix this but I'm in favour of a more linear percentage increase, e.g. Missiles_2 to Missiles_5 each granting an additional +15% increase. So I'd simply hardcode them as 115%, 130%, 145%, 160%. Yeah, it means pilots with Missiles_5 for example will have no use of Missiles_2 since the higher value overrides it (assignment instead of increment) but that's how the skill tree works anyway: a pilot can't get Missiles_5 without Missiles_2.

And if you rearrange the trees to give some pilots the higher skills while skipping the lower skills, a straight-up assignment works better anyway as the calculation I showed above shows - i.e. any pilot who has Missiles_4 will be guaranteed to get a 30% bonus instead of losing 15% due to skipping Missiles_2 and Missiles_3. That way you don't need to clutter the skill trees with the previous skills.

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I think the anti-ECM bonuses are similarly screwed up, and I need to take a look at the unguided missiles ("rockets") as well.