If your still looking for some encounter ideas I have a few.
The Gunners: It would be a large project but after you're defeated by gunners you could embark on a more explicit version of Slavetown for NV. I think the menial side of that mod pays dividends in immersion and it could be made more interesting with sadistic overseers trying to outdo each other in cruelty. And you yourself could either try to liberate the slave population, become an informer to the overseers or just try to work yourself up to prominence within the slave faction.
Children of Atom: Linking to your idea of Radiation Mutagens, they take you to their main base, perhaps the lighthouse on the north-east coastline, or their other settlement slightly to the north of that. Not exactly sure how this quest line might progress, perhaps they discover, after initially treating you like a animal that you develop a condition or grow a appendage from the radiation which marks you as a the Chosen One in their religion(not knowledgeable of the lore) and you are risen to the position of High Priestess, but must content with all the bizarre trappings that entails.
Brotherhood of Steel: If you choose one of the other factions than the BoS they will try to capture you for your treachery, they will then use you as test subject for the technology they find in the commonwealth. And if this is possible perhaps they could take you out on their Vertibird missions, suitably bound with a blow-up collar they might send you into supermutant/raider camps as bait, you then have to make it back to the Vertibird without getting caught in the crossfire.
I realise this was not exactly what you were asking for but wanted to get the ideas down on paper, so to speak.
