1. The method "SetAllowCombat" is pretty self-explanatory. If it is false then you're obviously making it so the npc cannot go into combat since that's what it does. Making the NPC passive isn't hard at all, take the target dummy into account here. You can attack it, but it cannot attack back. I would say edit its flags but it seems you've had trouble with that. When it is stunned/pacified the combat animation should be suppressed seeing it isn't ready to attack yet. The only thing I see here is changing its react state to passive, like pets for example.
However, I don't think we even have React states in Eluna at the moment. I think what's holding us back is that cMangos classic has their ReactState in Unit CharmInfo and TC's is in Creature (not in CharmInfo), leaving us to add completely different methods just for them being so different. We could always add it to one emulator but not the other, however, that isn't the ideal thing to do. Creature inherits unit allowing it to access 'CharmInfo()->REACT_FUNCTIONS', but again, either way, it would be a bust.
REACT_PASSIVE = 0,
REACT_DEFENSIVE = 1,
REACT_AGGRESSIVE = 2
2. You can search the source or if you have VS up, search for "SetStandState" -> Right Click -> Go To Definition and you should see the enumerator type "UnitStandStateType" -> Right Click -> Go To Definition. OR you can read this: It is in "Unit.h" under "enum UnitStandStateType". When Eluna is documented more, you will be able to go to Eluna's wiki to view all of this: "http://eluna.emudevs.com/"
3. I'm pretty sure there is, but I not sure of this. Perhaps someone can help you with this.
4. Ever since I added vehicles to Eluna they have always been a pain and buggy. However, that was awhile ago and they should work. I can't give any examples at the moment.