the great khans hate me (vilified actually) so I please help I'm getting really annoyed.
That could be the issue, I know with the powder Ganger's if you are vilified you cannot do the quests in the NCR prison. The regular characters won't mind you being there if you wear their armor, but all the quest characters see through your disguise and attack you. Try doing some other Khan side quests (If you can) and raise your reputation with them and see if that helps.
When I first started the game I didn't realize the whole faction set up of the game and the first mission I did set the Powder Gangers in a bad light, so I started killing them all when I would go to one of their settlements or the ones around the prison thinking they were the enemy, little did I know it was just because I was wearing an NCR face mask lol