Two more thoughts about notes and user markup (for this and any other text has canonical version, and that is heavily commented):
It might make sense not to put the notes in a verse-specific (or chapter-specific) tiddler within a notes field.
Multiple reasons:
(1) Notes may correspond to a range (such as the set of verses corresponding to a paragraph — and you don’t have tiddlers for paragraph, though you could…), and may also be comparative in less local ways. Instead of a “compare to [[link here]]
passage” located at one tiddler, a thematic "look at differences among [[this]]
and [[that]]
and [[the other]]
" would not be tied to any one of them, but would be displayed on a view template that looks for backlinks (or the notes tiddlers have a field for verse details, etc.)
(2) relating to the shadow-tiddler issue: restoring-to-shadow would delete notes, but you might want something like a restore-kjv-content-to-shadow to be available without losing user notes.
Another thought: this is a case where some tool for semantic highlighting might really be in demand. How to store the highlighting info, toggle display on and off, assign colors and other style info, and make something like a user-configurable semantic key for the various classes involved…? Highlights, like textual notes, may ultimately deserve their own tiddler with metadata (highlighted when, by what user, with what semantic class…)
This also might be a case where something like the keywords plugin — that holds the keywords outside of the target tiddlers (sorry I can’t find it here) — would be a natural fit.
Of course, @Scott_Sauyet, this shouldn’t turn into a “no good deed goes unpunished” adventure… You might not want to tackle any of this yourself! But thinking about a showcase edition, it strikes me that there are many texts (including some in my academic field) that attract close reading, where your KJV project can illustrate best design practices for holding canonical content alongside user marks/notes.
Especially ambitious reach for future project embellishment: canonical text structural tiddlers can toggle display between different translations, or show them side by side.