For the reference indicators, I found an interesting way to handle them: NBA Bulletin 51 (Winter '15-'16) p. 11. Since all bold words and phrases have notes associated with them the Bulletin suggests to insert a note on the TN Page: All words in bold have notes associated with them. The notes are placed at the end of the print page. This eliminates the need for any reference indicator. Presently, the only other bolded words are paragraph headings in very short exercises, where the emphasis was changed to italics, making vocabulary the only bolded items in the text.
Scenes/Directions in print are blocked, which I'll retain but this leaves many blank lines. There are often 3-5 different and consecutive directions, all different. A blank line is also used between directions and dialogue.
The only other big question I have that I forgot to include concerns the note separation line and the page change indicator. Should these note separation lines be separated from Dialogue/Directions-Settings at the end of the print page? In plays, it seems that everything is separated, dialogue from directions, etc. A blank line makes the change in context clear because on the following page both dialogue and notes continue in most cases and its confusing as to which the text on the next page is a continuation of, dialogue or notes. I've attached 3 images with different formats but am not sure which format is the best. I visually prefer image B which makes the distinction clear.
Thanks for your input, it was very helpful, especially about the soon-to-be footnote guidelines.