Agree with Jeff about Rules By Topic (which gathers the various rules, or parts of rules, from all over the RB into one place for selected topics). If you're struggling with making the associations between the bits and pieces of the rules that are spread across the book, this may be of great help to you in learning the rules.
As for applying them, there really is no substitute for simply getting out on the floor and calling games. The rule book can clearly define what a foul is in text, but you've got to learn to recognize a foul in game situations. Honestly, that comes from seeing lots of plays, screwing some of them up, going back to the books and having discussions with other officials (like happens here), and then seeing those plays again and applying what you learned.
As for a framework, I know it's not really what you were envisioning, but if you're working a decent level of ball where the players and coaches and your partners have a reasonable amount of experience, a simple framework is simply that you do the best job you can and "they" will let you know when you're messing up. That's not to say that just because a coach questions a call/no-call you got it wrong. But if you consistently are getting grief for how you call certain plays, you probably need to reevaluate how you calling them.
Just my $0.02
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"It is not enough to do your best; you must know what to do, and then do your best." - W. Edwards Deming
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