Factions hate me for no reason

[ChocomintCA]

I decided to replay FONV and I got up to the quest where the NCR wants me to take care of the BoS, and I'd rather not kill them (mostly because I can't.) I do have a mods like Warzones and Increased Wasteland Spawns, but the only time I've ever encountered them (before the quest) was a small 'patrol' near Bonnie Springs, and I killed them. But it was in self defense, I'm sure they'd understand. I am idolized by the NCR, and I do have Boone as a follower, and I'm wearing Customized Ranger Armour (from A Definitive Armour Mod), but I switched to faction-less clothing and told Boone to go do nothing at the Lucky 38. The map icon for Hidden Valley says it's Neutral, which it should be, but every time they burst through the door they cut me down in under half a second. I really haven't done much to provoke any faction other than the Legion, and I technically just met the BoS, since the other soldiers were modded.

 

I guess a possible solution would be to simply start a new game but I'd rather not lose 35 ish hours and have to redo tedious quests. I have tried some console commands to remove Infamy and give me more Fame with the BoS faction but it apparently does nothing. I had a similar problem with the Great Khans, even though I helped them in Boulder City. Whenever I check the General Tab for faction reputations I don't see the BoS or the Great Khans. I've only seen the BoS in that tab after it said they hated me. With the Khans it seemed like the 'original' NPCs wandering around their canyon had no problem with me, but the IWS (I'm assuming) placed guards and patrols hated me. Papa Khan hated me too though, so I'm not sure what to think about that. I didn't have much contact with the Khans before the quest other than the Boulder City Showdown, but I'm sure they wouldn't have tried to kill me. Maybe it has something to do with the quest?

 

I googled the problem and somebody suggested using a faction disguise, the only problem is they strip me naked after talking and obliterate me instantly. I got past that small problem and spawned me in some more Elder robes but Paladin Ramos, or whoever that guy is, shoots an Elder on sight. I ran past him but I can't really go anywhere else (I think).

 

Is there anything that can be done to fix the quest/faction/whatever-the-problem-is?