Great stuff here. Many thanks for doing this!
Here's something I found:
On Stormweaver.md, Hexbinder.md and Stormshifter.md files, there's a "---" line with a "###" just after. That can give issues to some plugins (it did for me).
On \Equipment\Item Sets\Mystic Michael's Myriad of Marvelous Machinations\Tome of Summon Cat.md, there's a reference to [Kissy the Cat] which I couldn't find.
And finally, because I'm on Windows, three files changed the names from "?" to "_", and made these references fail too: [That all you got?!] on Berserker.md, [What? I've Been Around] on Backgrounds.md and [How'd YOU get here?!] on The Cheat.md.