Hey all!
Thanks for including me in this discussion, I love this topic and I’m excited to see a sort of amalgamation of all sorts of open access journals!
Whenever I’m discussing an academic paper with my students, I’ll pull up the paper on my projector screen and walk through it, showing them that even I have to stop and make sure I understand a particular piece of jargon, or to interpret a graph. I think this kind of modeling is critical because it helps students understand that it’s really like learning another language, to sift through scientific terminology that’s relatively unfamiliar; they shouldn’t expect themselves to just dive in and understand every facet of the information!
That being said, I really love the methods you’ve shared, @llundgren and all, on breaking a paper down into manageable chunks.
I’m pretty sure I found this image through a thread on myFOSSIL, but here it is anyway (see attached) – Jennifer Raff has some great tips on how to begin deciphering an academic paper, and I’ve used this graphic with my students with some pretty good success, as a baseline.
As far as the anatomy goes – man, there’s the other language, and in this case it really is learning to decipher Latin and Greek, of course…so I’d start students with a diagram of a modern beaver skull, like this one: 
…So they can become familiar with the “map” of a skull, and I’d probably lead them through it by translating most of the words into something a bit clearer. Though, I’ve found with a lot of my ESL students, especially Spanish-speaking students, that the Latin terms often help them remember what each feature is.
Whew! Happy to chat more about this. (Also, if I may gush for a moment – what a freaking cool beaver paper! :D)
Best wishes, all.
Tara