Thank you for posting this, Kellus. I haven't gone through all of it yet, but it's a very, very interesting system that I will be using, at least for world building and awesome loot for the players to find (the world's tech level fell severely in the past millenia).
While I am still going through all of this (and as such can't really help with new ideas), I can at least help with a Table of Contents. It doesn't have the custom blueprints from the thread, but I tried to grab everything else:
EDIT: Index updated - check page 16.
I opted to group the Discoveries and Theories under the Gramarist base class instead of making a "Character Options" section, simply because they appear to be options solely for that class (both are listed as class features). Otherwise, it's all alphabetized, and I can grab the blueprints from the thread if there is a need for it.