Some brief history, I'm honestly stumped over this one:

Meet 1, Sept
We arrange casual lunch, it turns into dinner, we argue at the restaurant but I later kclose during the ride home. More calls/emails, second date is arranged, she flakes out, I send her a pissed message and later drop her from the phonebook.

Meet 2, Yesterday
She messages me happy bday in Jan, emails/calls start up again, she now has an unofficial bf. April, we arrange for her to help me with a bit of math. She comes by (y'day) and stays for the whole day. Kclose as she leaves (she tells me no because I hadn't made the move sooner in the day, but she lets me kclose anyway). When she gets home she messages telling me to not "think for a second" that I get to do that every time I see her.

Question(s)
(1) She knows and uses 'the game' (she's been reading Strauss etc for ages). I learn't about the game yesterday. I've been a blatant AFC and I'm probably about to or already am slipping into the fzone. How do I prevent that from happening?

(2) She has a bf and my assessment is that she sees me as (potentially) a safe option/ guy to fall back on if it goes wrong with him. She moans about him and they're on a break but she clearly has the biggest hard-on for him. How can I get her to take me seriously and then replace him?

Look, no matter how much the girl studies about the GAME, it doesn't matter, it's not rocket science. It's Pavlov stimulus-response method, that mean you feeds her a stimulus, her brain will response in a certain way.
Doesn't matter if she's aware of it, her brain still responds and it still shows in her body languages. It's like I'm telling you I will hit you, and you know I will, and you will flinch. That's all.
Take the concept you learn and develop your own routines or pattern, as long as you don't use canned materials from the books, she will hardly be able to notice what you're doing it, or even if she does, she's already effected by it.

And I'd be glad to answer your question, but I'm still confused about your story.
But as I can tell, she hasn't used any counter - PUAs stuffs on you. She told you not to think about it, that's simply ASD. Watch her actions, not her words. It was obvious that she agreed to spend the whole day with you, and let you kclose regardless.

Cool, ok so I use the game anyway. The boyfriend thing is still a nuisance though, how am I to get rid of him? And how do I change this afc-pussyboy view she's developing of me?

Go game other girls, you can't transform overnight. You need experiences and practice.
Once you become good at what you do, I doubt you still want her, but let's say you still do, then you come back as a cooler guy with high social value, someone that can make her bf look like an AFC.

Be yourself right now. Your gonna fuck it up trying to run game since you don't much.