A Zoology of Annotations
I delimit italicized text with underscores. (I don't have any page-long italicized passages, so any such are probably due to loss of "underscore-parity".)
(The Clarinet edition supports italicized fonts, so this convention will probably be transparent to you.)
Embedded comments have "^ " as the first non-whitespace on the line. Commands to my formatter (inherited from Kernighan and Plauger's Software Tools, Addison-Wesley, 1976!) use a similar convention:
^bp page break
^ls n linespacing
^he s define page header
^fo s define page footer
etc.
My formatter prints the pair ampersand numbersign ( "&# " ) as a single numbersign ( "# " ). Thus, I use "&#&#&#" as a section break. When a numbersign ( "#" ) is not preceded by an ampersand, it is supposed to be a single space. (I use this character to force vertical whitespace and as part of the indent for paragraphs.)
Where the first alpha characters on a line are "NOTE", you are normally seeing a note to the copyeditor. (I use this mostly to flag the beginning of monospace font (eg, Courier) for the Net messages.)