Besides misusing PUA material, I think you're missing the big picture, here. For one, most of the material, while indeed some of it sleazy and/or not fit for everyone, isn't cheap.
Being a PUA is not all about stacking material non-stop, especially if you're not really comfortable with it or feel that "it's not the real you". That's why almost all PUA's suggest to their customers/friends to create their own routines based on a combination of what women perceive as attractive traits and your own unique personality and background ( in other words, being natural ).
From what I can tell, you had the right tools but the wrong Mindset. To answer your first question, at some level, you will continue to use the material provided by PUA's simply because you are aware of it. These are lines/routines that work if delivered right WILL get you the girl. KEEPING her, however, is another skill set, not that different, I might add. And you can grow beautiful relationships from PUA material too, I ( and many others on this forum ) have done it. It's just a matter of mindset.
As with how that went in your room, I can't really tell if she's a whack-job or you've pushed it too far. How much of a notch did you turn up? Did you guys just fell asleep or did she left? Give us as many details as possible. Even in my most AFC moments in bed, nothing like that has ever happened.
And to answer your second question, call her, see where you stand with her, however, DO NOT, I repeat, DO NOT apologize for what happened in your room.