Nick - From all my questions to my coach (thankfully he's a patient guy), here's what I know (or think I know). Bracing is installed mainly for two reasons - (1) structural reinforcement (protect glue joints, provide durability and crack resistance, etc); (2) to transfer/control vibration and flexibility. The bracing in many mass produced guitars was altered from the original designs to increase durability so manufacturers weren't dealing with complaints about guitars cracking, warping, etc. and to improve the efficiency of the manufacturing process. But it cost the guitar sound qualities. I won't be worrying about durability - this guitar won't be the one I take fishing or camping with me. Therefore, we're focusing on sound quality and a little on tradition and craftsmanship (and my education about guitars and making them).
All the braces will get tapered. Not all the braces will penetrate through the kerfing and sides. All the bottom braces will be notched into the sides, the X brace and transverse brace will be notched into the sides. I think that's all (I get confused). If I understand correctly, the scallops and taper of the braces are part of the sounding process, changing and altering the flexibility of the top in selected areas. Some of the end tapers on braces that are notched into the sides are done simply so they will be hidden behind the binding later. While the Martin plans we're using do provide dimensions for bracing, it appears those aren't set in stone and can vary based on the builder's preference. I will roughly taper the braces where they abut the X bracing, just to make it easier later. Other than that, all the final scallops and tapers are done after gluing and as part of the sounding step. The top itself can also get some more sanding as part of sounding the top. It's a fascinating process for sure.
One thing I've learned, you can mechanically follow a set of plans or videos and build a perfectly functional, attractive guitar. But there are steps where the art or magic come into play that differentiate a really good sounding guitar from a mass produced guitar. That's where my coach is proving so valuable and I'm sure glad he agreed to help me.