Would you be able to post an copy of your print? It would certainly be helpful. I am trying to understand why you would place a TN "in the middle of 5/3 diresctions". Transcriber's notes are always placed in 7/5, apart from the exception in Nemeth of 7 or fewer words, which may be embedded within the text (not on a new line).
In your 2nd question, does the note pertain to the main item, or to the subdivision? I really need to see the print in order to determine how best to handle this.