Mystical Panda, Thanks, I sort of understand that if I entered data into GECK I may understand it, but, it's say, repairing a quest, or Mods Responses to Player karma/factions stance, I was hoping, that it could give world wide links/characters/items/locales/clues/responses but Obviously More Study of Geck may be answer ..
Scripts are powerful if they have a engine to do "grunt" work for them, I always admired Sid Meier's Coding, In Lots of Games, but especially in Gettysburg, its a Text file driven masterpeice, of it's time ..
I am suspect & hope these "layers" of Fallout Game's "OS", that "Do the work", are/is a similar concept, I may get my head around this, yet !!
With quests, the scripting engine often uses a 'quest' just to allocate and hold variable data that is referenced by other scripts; a 'global' in a way. To fix a quest, if it's possible, you'll need to know which variables to set or reset for the quests (or quests if they're linked together), and at the most simplest- which 'stage' to set or clear. It's hard to tell if there's a 'cascading' effect data wise; some you can 'reset' others you can't.
The Karma and stances would either be pseudo 'global' data embedded in a script or script fragment, or is checked using a specific scripting command. The command is either vanilla or available through the script extender, or one of it's associated plugins (like JIPNVSE).
I don't think the scripting engine is the most efficient, and you can tell script heavy games or scripts that crank out in a tight loop instead of being 'event' driven; it's start tanking ever downwards.
Good luck, and look forward to checking out your mods!