I've been searching the net, this forum and the CK for what controls the 'hitmen' that are sometimes sent after you for the crime of Stealing.

I'd like to use this event or rather create one similar to it (if I can) that tracks the player for being a Vampire. This way I can create Witch Hunters and Vigilants that hunt you down for being a Vampire.

Cue the Silver Hand and those other guys whose name evades me for the moment...

I think you would need to tell the AI Package to have a condition to look for a GetDisease or maybe GetFaction, something similar along those lines.

What about a Quest that starts silently based on when the PC gains say a certain Perk that only Vampires would have?

Maybe you're right and it's easier just to edit the AI Package.

Check out the story manager on the wiki, you can trigger a quest from various game events in there.