So here's my line of thinking. The OS story, as a whole, is about how everyone, including John Nash, looks at what John Nash is lacking. He doesn't like people and people don't like him. He's lacking an original idea. He doesn't have a strong grasp of reality, etc. But should they all put up with him anyway? Should they permit him through to the next level even though he hasn't published anything? Should they put up with him even though he's kind of a jerk? So thematically, I think that looks like Deficiency vs Permission.
John's MC story is about John looking for recognition, but he has moments of Doubt, like when he bashes his head on the window, or he is doubted by others, like Hansen who treats him like the waiter and then tells him he'll fail. But that's countered by his constant exploration of math, his constant search for answers to difficult problems. Doubt vs Investigation.
Charles and Parcher will be a bit more difficult to describe, but Parcher mostly has John attempting to break codes in order to find a bomb that the Russians plan to detonate over America. Charles tells John to go on, bust his head. Keep working. Whatever the scene, they are always pushing him in regards to Attempt vs Work.
The relationship is probably beyond me to try to explain, but it would be locked in at Preconditions vs Prerequisites. Preconditions. Maybe that John needs to be stressed to trigger his vision? Vs not taking his meds? I don't really know. I want to say they feel right, but that's not particularly helpful.
So back to OS. Everyone is sort of driven to evaluate John. Is he good enough? Smart enough? Does he have anything to offer? In the scene with the blond problem, they are evaluating previous mathematical theories. Nash evaluates the class as being a waste of the students, and, infinitely worse, his time. Alicia needs to know what's wrong with him, doesn't want to accept the evaluation of Schizophrenia. The problem is solved when John reevaluates the reality of his friends.
In the MC, John's work is being evaluated at Princeton. He evaluates the others on the magazine cover as not worthy to be on the cover with him. And, of course, everyone evaluates him as crazy. This problem is solved not only when he reevaluates the reality of his friends, but when people like Hansen stop seeing him as a jerk and start seeing him as an old friend, or stop looking at how he's crazy and at how his life's work is worthy of recognition.
Charles and Parcher work through Reduction. Paraphrashing Charles-"It's not your problem, it's theirs. The answer isn't here looking at the wall, it's out there." Parcher has him reducing paper and magazine articles to code to determine what they mean. They don't want to be reduced/ignored out of Johns life.
That selection gives us the OS Plot progression you've already mentioned of Conceiving, Being, Becoming, Conceptualizing.