Wow. Kudos for taking this on! Are you using the ligature symbol for anything? That would certainly be an option for either the upper or lower ligatures. I do think they are separate things and should be transcribed differently. You could always include a TN that says that words connected by ligature marks have spaces between them in print. The point is that they are being pronounced as one word even though they are two separate words, right?
For the words with crossed out or underlined letters: I do think showing them once without any additional marks (including ligatures) and then repeating them would be helpful for the reader. I would show the whole phrase/sentence that way for context.
As for TN's. Put one on the TN page - and then put a TN at the FIRST instance within the text...but don't repeat it every time.
Does that answer all your questions?
Cindi