Are there direct references to or quotes from Charles Manson and his followers in MM's work?
Yards of them. "I am the God of Fuck" was originally a line of Charlie's. The main verse of My Monkey is taken from Manson's song Mechanical Man. The demo track Dune Buggy opens with a quote from Family member Tex Watson (and seems to be about Manson and the Family). Samples of Charlie speaking appear on the cassette releases, and some of the same passages used to be recited by Mr. Manson during shows ("I play music. People are affected by the music I play. That doesn't mean I direct traffic! That doesn't mean I put a knife in anyone's hand and tell 'em to go kill somebody!" seems to have been a favorite.)
The titles "Big Black Bus" and "The Family Jams" are both Manson-related: the Family drove a black (VW) bus, and The Family Jams was the name of the rock group made up of clan members which Charlie tried to organize and manage. And Manson's physical image (especially his eyes) has been used in the band's advertising and t-shirts, both by them directly and by others. Also, both MWG and Twiggy have been known to draw a small black X between their eyes, as Charlie and the female Family members did during their trial.
There's also a visible degree of Family influence in the Reverend's formal oratory. While only a close search of the volumes of written material on Charlie and the Family would locate every possible reference, here's a sample or two.