One very important thing you will need to know before proceeding is that right now your better off putting no docked entities on any of the ships your NPC faction will be using. They will shed their turrets and leave them EVERYWHERE.
Another thing you should avoid are scavenger fleets, these are sent out any time a player's behavior results in an entity, any entity overheating. The behavior that regulates fleets does not exercise any solid and absolutely necessary things like retreat conditions. Instead NPC factions will stuff your home sector like a clown car until your frame rate drops to nil, or necessitating you to constantly run the command to clear out npcs, both of which will annoy you to exhaustion and rage. Often after arriving, these ships will then proceed to completely render themselves inert and just sit there despite them being undamaged or messed with in any way. Your better off simply turning this feature off, it's on line 892 of the NPCconfig.xml:
<ScvengingFleetsPerTurn>6<!--Amount of sectors to target with scavengin fleets (sectors where an attack happened in range)--></ScvengingFleetsPerTurn>
Replace the 6 with a big fat zero and you or the people on the server won't have to deal with any of this nonsense. At one point I even turned it down to 1 and it was too much for most people, which is really quite sad, as I was hoping this aspect would enrich game play. As it is, it's too poorly implemented to be allowed to exist. Trust me when I say your better off without it.
Another smart thing would be to alter the settings on lines 790 to 796, which regulates how often the NPC faction conducts diplomacy checks. Vanilla settings run the check every minute or as in the config, 60000 milliseconds. I recently changed the NPC configs on LvD from the vanilla 1 minute to 15 minutes and I've noticed smoother server operation and significantly less garbage when monitoring via console. Hhere what the lines look like:
</Diplomacy>
<DiplomacyStatusCheckDelay>60000<!--Check for status effects (war, etc)--></DiplomacyStatusCheckDelay>
<DiplomacyTurnEffectDelay>60000<!--Time for turn effects to apply to points--></DiplomacyTurnEffectDelay>
<DiplomacyTurnEffectChangeDelay>60000<!--Time for turn effects to change (falloff or get stronger depending on direction)--></DiplomacyTurnEffectChangeDelay>
If anyone else has some tricks they have used to make this feature in it's current state usable please let me know and contribute to this thread.
This can help raise awareness of the issues and hopefully speed the fixes this feature badly needs.