>help me refine my ability to actually take in what I'm reading on an academic level
This is how you do it: you first read it superficially without paying much attention to semantics. Focus on prose and its aesthetics. This is your first read. Now comes the second read, wherein you analyse. How do you approach analysis of a text?
Roughly:
1. Read the n sentence.
2. Stop; think, though in not much detail, about what it means or what it might mean and how it relates to previous, n - 1, n - 2, ..., n - (n - 1), sentences (unless it is the very first, n = 1, sentence of the book).
2.1. Use various formal methods, tools, and techniques to look at the lexical, logical, and semantical structure of the sentence. If it happens that there are one or more quantifiers, see what the scope of the bound variable(s) is, what domain of discourse it ranges over, and so on. Every time a character is introduced, give it a name (could be as simple as "a" or "b", or its actual name in the novel) and add him to the domain of discourse. Axiomatize its character by predicating whatever adjectives and epithets are appropriate; since there are events in the novel, preferably, you do it temporally: to each predicate you also ascribe a time coordinate to keep track of the character over time; whether it changes or not, and if so, how, when, and why, did the character change)
2.2. By Logic alone, see if you can derive any corollaries from that sentence. If you can't derive much by Logic alone, see if the sentence suggests or conversationally implicates (not to be confused with implication a.k.a. the material conditional of Logic) things in the novel.
2.3. Based on fragmentary information (say, first Chapter of the book), posit hypotheses about characters or how the story will unfold early in the book: you can use probability, decision theory, game theory, or 'possible worlds' semantics of Modal Logic
2.4. Read the n + 1 sentence, and repeat the process outlined above.
Formalising all of the novel is somewhat unrealistic but that's one way of doing it. It's effective and helps you internalise much of its content, relationships among its characters and events.
Tl;dr: just fucking use and apply whatever you learned in STEM to literature. It's not that hard. But obviously, discrete maths and various logics and calculi are better suited for this than continuous maths. If you do it correctly (be as autistic as you can about it), you'll retain most of it.